135 results on '"Savvides SN"'
Search Results
2. The crystal structure of Nictaba reveals its carbohydrate-binding properties and a new lectin dimerization mode.
- Author
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Bloch Y, Osterne VJS, Savvides SN, and Van Damme EJM
- Abstract
Nictaba is a (GlcNAc)n-binding, stress-inducible lectin from Nicotiana tabacum that serves as a representative for the Nictaba-related lectins, a group of proteins that play pivotal roles in plant defense mechanisms and stress response pathways. Despite extensive research into biological activities and physiological role(s) of the lectin, the three-dimensional structure of Nictaba remained largely unknown. Here, we report crystal structures for Nictaba in the apo form and bound to chitotriose. The structures reveal that the Nictaba protomer has a jelly-roll fold, similar to the cucumber lectin Cus17, but exhibit a unique and previously unseen mode of dimerization. The chitotriose binding mode, similar to Cus17, centers around the central GlcNAc residue, providing insights into the determinants of specificity of Nictaba towards carbohydrate structures. By integrating these structural insights with inputs from glycan arrays, molecular docking, and molecular dynamics simulations, we propose that Nictaba employs a single carbohydrate-recognition domain within each of the two subunits in the dimer to display pronounced specificity towards GlcNAc-containing carbohydrates. Furthermore, we identified amino acid residues involved in the extended binding site capable of accommodating structurally diverse high-mannose and complex N-glycans. Glycan array and in silico analyses revealed interactions centered around the conserved Man3GlcNAc2 core, explaining the broad recognition of N-glycan structures. Collectively, the structural and biochemical insights presented here fill a void into the atlas of lectin structure-function relationships and pave the way for future developments in plant stress biology and lectin-based applications., (© The Author(s) 2024. Published by Oxford University Press.)
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- 2024
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3. Clostridium perfringens chitinases, key enzymes during early stages of necrotic enteritis in broiler chickens.
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Dierick E, Callens C, Bloch Y, Savvides SN, Hark S, Pelzer S, Ducatelle R, Van Immerseel F, and Goossens E
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- Animals, Necrosis, Intestinal Mucosa microbiology, Intestinal Mucosa metabolism, Bacterial Proteins metabolism, Bacterial Proteins genetics, Clostridium perfringens enzymology, Clostridium perfringens pathogenicity, Chickens microbiology, Chitinases metabolism, Chitinases genetics, Poultry Diseases microbiology, Clostridium Infections microbiology, Clostridium Infections veterinary, Enteritis microbiology
- Abstract
The interaction between bacteria and the intestinal mucus is crucial during the early pathogenesis of many enteric diseases in mammals. A critical step in this process employed by both commensal and pathogenic bacteria focuses on the breakdown of the protective layer presented by the intestinal mucus by mucolytic enzymes. C. perfringens type G, the causative agent of necrotic enteritis in broilers, produces two glycosyl hydrolase family 18 chitinases, ChiA and ChiB, which display distinct substrate preferences. Whereas ChiB preferentially processes linear substrates such as chitin, ChiA prefers larger and more branched substrates, such as carbohydrates presented by the chicken intestinal mucus. Here, we show via crystal structures of ChiA and ChiB in the apo and ligand-bound forms that the two enzymes display structural features that explain their substrate preferences providing a structural blueprint for further interrogation of their function and inhibition. This research focusses on the roles of ChiA and ChiB in bacterial proliferation and mucosal attachment, two processes leading to colonization and invasion of the gut. ChiA and ChiB, either supplemented or produced by the bacteria, led to a significant increase in C. perfringens growth. In addition to nutrient acquisition, the importance of chitinases in bacterial attachment to the mucus layer was shown using an in vitro binding assay of C. perfringens to chicken intestinal mucus. Both an in vivo colonization trial and a necrotic enteritis trial were conducted, demonstrating that a ChiA chitinase mutant strain was less capable to colonize the intestine and was hampered in its disease-causing ability as compared to the wild-type strain. Our findings reveal that the pathogen-specific chitinases produced by C. perfringens type G strains play a fundamental role during colonization, suggesting their potential as vaccine targets., Competing Interests: SP and SH are employees from Evonik Nutrition & Care., (Copyright: © 2024 Dierick et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
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- 2024
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4. The pros and confs of IL-18 activation.
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Clancy DM, Andries J, and Savvides SN
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- Humans, Animals, Protein Processing, Post-Translational, Interleukin-18 metabolism, Interleukin-18 immunology, Signal Transduction immunology
- Abstract
Interleukin-1 (IL-1) family cytokines are key immunological regulators that achieve their signaling prowess after post-translational proteolytic processing. In this issue of Immunity, Dong et al. reveal the structural consequences of this process on proinflammatory IL-18, demonstrating that pro-IL-18 and mature IL-18 are structurally distinct., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Inc. All rights reserved.)
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- 2024
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5. Structures of complete extracellular receptor assemblies mediated by IL-12 and IL-23.
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Bloch Y, Felix J, Merceron R, Provost M, Symakani RA, De Backer R, Lambert E, Mehdipour AR, and Savvides SN
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- Humans, Animals, Mice, Interleukin-23, Cytokines metabolism, Receptors, Cell Surface, Interleukin-12, Signal Transduction physiology
- Abstract
Cell-surface receptor complexes mediated by pro-inflammatory interleukin (IL)-12 and IL-23, both validated therapeutic targets, are incompletely understood due to the lack of structural insights into their complete extracellular assemblies. Furthermore, there is a paucity of structural details describing the IL-12-receptor interaction interfaces, in contrast to IL-23-receptor complexes. Here we report structures of fully assembled mouse IL-12/human IL-23-receptor complexes comprising the complete extracellular segments of the cognate receptors determined by electron cryo-microscopy. The structures reveal key commonalities but also surprisingly diverse features. Most notably, whereas IL-12 and IL-23 both utilize a conspicuously presented aromatic residue on their α-subunit as a hotspot to interact with the N-terminal Ig domain of their high-affinity receptors, only IL-12 juxtaposes receptor domains proximal to the cell membrane. Collectively, our findings will help to complete our understanding of cytokine-mediated assemblies of tall cytokine receptors and will enable a cytokine-specific interrogation of IL-12/IL-23 signaling in physiology and disease., (© 2024. The Author(s), under exclusive licence to Springer Nature America, Inc.)
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- 2024
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6. Activation of goblet-cell stress sensor IRE1β is controlled by the mucin chaperone AGR2.
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Cloots E, Guilbert P, Provost M, Neidhardt L, Van de Velde E, Fayazpour F, De Sutter D, Savvides SN, Eyckerman S, and Janssens S
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- Endonucleases, Protein Disulfide-Isomerases, Humans, Cell Line, Tumor, Goblet Cells metabolism, Molecular Chaperones genetics, Mucins genetics
- Abstract
Intestinal goblet cells are secretory cells specialized in the production of mucins, and as such are challenged by the need for efficient protein folding. Goblet cells express Inositol-Requiring Enzyme-1β (IRE1β), a unique sensor in the unfolded protein response (UPR), which is part of an adaptive mechanism that regulates the demands of mucin production and secretion. However, how IRE1β activity is tuned to mucus folding load remains unknown. We identified the disulfide isomerase and mucin chaperone AGR2 as a goblet cell-specific protein that crucially regulates IRE1β-, but not IRE1α-mediated signaling. AGR2 binding to IRE1β disrupts IRE1β oligomerization, thereby blocking its downstream endonuclease activity. Depletion of endogenous AGR2 from goblet cells induces spontaneous IRE1β activation, suggesting that alterations in AGR2 availability in the endoplasmic reticulum set the threshold for IRE1β activation. We found that AGR2 mutants lacking their catalytic cysteine, or displaying the disease-associated mutation H117Y, were no longer able to dampen IRE1β activity. Collectively, these results demonstrate that AGR2 is a central chaperone regulating the goblet cell UPR by acting as a rheostat of IRE1β endonuclease activity., (© 2023. The Author(s).)
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- 2024
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7. Ym1 protein crystals promote type 2 immunity.
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Heyndrickx I, Deswarte K, Verstraete K, Verschueren KHG, Smole U, Aegerter H, Dansercoer A, Hammad H, Savvides SN, and Lambrecht BN
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- Animals, Humans, Mice, Adjuvants, Immunologic, Crystallization, Inflammation, Adaptive Immunity, Chitinases
- Abstract
Spontaneous protein crystallization is a rare event, yet protein crystals are frequently found in eosinophil-rich inflammation. In humans, Charcot-Leyden crystals (CLCs) are made from galectin-10 (Gal10) protein, an abundant protein in eosinophils. Although mice do not encode Gal10 in their genome, they do form pseudo-CLCs, made from the chitinase-like proteins Ym1 and/or Ym2, encoded by Chil3 and Chil4 and made by myeloid and epithelial cells respectively. Here, we investigated the biological effects of pseudo-CLCs since their function is currently unknown. We produced recombinant Ym1 crystals which were shown to have identical crystal packing and structure by X-ray crystallography as in vivo native crystals derived from murine lung. When administered to the airways of mice, crystalline but not soluble Ym1 stimulated innate and adaptive immunity and acted as a type 2 immune adjuvant for eosinophilic inflammation via triggering of dendritic cells (DCs). Murine Ym1 protein crystals found at sites of eosinophilic inflammation reinforce type 2 immunity and could serve as a surrogate model for studying the biology of human CLCs., Competing Interests: IH, KD, KV, KV, US, HA, AD, HH, SS, BL No competing interests declared, (© 2023, Heyndrickx et al.)
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- 2024
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8. Protein citrullination and NET formation do not contribute to the pathology of A20/TNFAIP3 mutant mice.
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Van Damme KFA, Hertens P, Martens A, Gilis E, Priem D, Bruggeman I, Fossoul A, Declercq J, Aegerter H, Wullaert A, Hochepied T, Hoste E, Vande Walle L, Lamkanfi M, Savvides SN, Elewaut D, Lambrecht BN, and van Loo G
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- Humans, Animals, Mice, Citrullination, Tumor Necrosis Factor alpha-Induced Protein 3 genetics, Tumor Necrosis Factor alpha-Induced Protein 3 metabolism, Inflammation metabolism, Autoimmunity genetics, Arthritis, Rheumatoid metabolism, Lupus Erythematosus, Systemic genetics, Lupus Erythematosus, Systemic metabolism, Extracellular Traps metabolism
- Abstract
A20 serves as a critical brake on NF-κB-dependent inflammation. In humans, polymorphisms in or near the TNFAIP3/A20 gene have been linked to various inflammatory disorders, including systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA). Experimental gene knockout studies in mice have confirmed A20 as a susceptibility gene for SLE and RA. Here, we examine the significance of protein citrullination and NET formation in the autoimmune pathology of A20 mutant mice because autoimmunity directed against citrullinated antigens released by neutrophil extracellular traps (NETs) is central to the pathogenesis of RA and SLE. Furthermore, genetic variants impairing the deubiquitinase (DUB) function of A20 have been shown to contribute to autoimmune susceptibility. Our findings demonstrate that genetic disruption of A20 DUB function in A20 C103R knockin mice does not result in autoimmune pathology. Moreover, we show that PAD4 deficiency, which abolishes protein citrullination and NET formation, does not prevent the development of autoimmunity in A20 deficient mice. Collectively, these findings provide experimental confirmation that PAD4-dependent protein citrullination and NET formation do not serve as pathogenic mechanisms in the development of RA and SLE pathology in mice with A20 mutations., (© 2023. Springer Nature Limited.)
- Published
- 2023
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9. Rare Antagonistic Leptin Variants and Severe, Early-Onset Obesity.
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Funcke JB, Moepps B, Roos J, von Schnurbein J, Verstraete K, Fröhlich-Reiterer E, Kohlsdorf K, Nunziata A, Brandt S, Tsirigotaki A, Dansercoer A, Suppan E, Haris B, Debatin KM, Savvides SN, Farooqi IS, Hussain K, Gierschik P, Fischer-Posovszky P, and Wabitsch M
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- Child, Humans, Antibodies, Homozygote, Signal Transduction, Leptin genetics, Obesity, Morbid genetics
- Abstract
Hormone absence or inactivity is common in congenital disease, but hormone antagonism remains controversial. Here, we characterize two novel homozygous leptin variants that yielded antagonistic proteins in two unrelated children with intense hyperphagia, severe obesity, and high circulating levels of leptin. Both variants bind to the leptin receptor but trigger marginal, if any, signaling. In the presence of nonvariant leptin, the variants act as competitive antagonists. Thus, treatment with recombinant leptin was initiated at high doses, which were gradually lowered. Both patients eventually attained near-normal weight. Antidrug antibodies developed in the patients, although they had no apparent effect on efficacy. No severe adverse events were observed. (Funded by the German Research Foundation and others.)., (Copyright © 2023 Massachusetts Medical Society.)
- Published
- 2023
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10. Correction to: Unexpected complexity of the ammonia monooxygenase in archaea.
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Hodgskiss LH, Melcher M, Kerou M, Chen W, Ponce-Toledo RI, Savvides SN, Wienkoop S, Hartl M, and Schleper C
- Published
- 2023
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11. Improving de novo protein binder design with deep learning.
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Bennett NR, Coventry B, Goreshnik I, Huang B, Allen A, Vafeados D, Peng YP, Dauparas J, Baek M, Stewart L, DiMaio F, De Munck S, Savvides SN, and Baker D
- Subjects
- Protein Engineering, Proteins metabolism, Protein Binding, Deep Learning
- Abstract
Recently it has become possible to de novo design high affinity protein binding proteins from target structural information alone. There is, however, considerable room for improvement as the overall design success rate is low. Here, we explore the augmentation of energy-based protein binder design using deep learning. We find that using AlphaFold2 or RoseTTAFold to assess the probability that a designed sequence adopts the designed monomer structure, and the probability that this structure binds the target as designed, increases design success rates nearly 10-fold. We find further that sequence design using ProteinMPNN rather than Rosetta considerably increases computational efficiency., (© 2023. The Author(s).)
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- 2023
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12. Pore-forming proteins as drivers of membrane permeabilization in cell death pathways.
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Vandenabeele P, Bultynck G, and Savvides SN
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- bcl-2-Associated X Protein metabolism, Cell Membrane metabolism, Membranes metabolism, Apoptosis
- Abstract
Regulated cell death (RCD) relies on activation and recruitment of pore-forming proteins (PFPs) that function as executioners of specific cell death pathways: apoptosis regulator BAX (BAX), BCL-2 homologous antagonist/killer (BAK) and BCL-2-related ovarian killer protein (BOK) for apoptosis, gasdermins (GSDMs) for pyroptosis and mixed lineage kinase domain-like protein (MLKL) for necroptosis. Inactive precursors of PFPs are converted into pore-forming entities through activation, membrane recruitment, membrane insertion and oligomerization. These mechanisms involve protein-protein and protein-lipid interactions, proteolytic processing and phosphorylation. In this Review, we discuss the structural rearrangements incurred by RCD-related PFPs and describe the mechanisms that manifest conversion from autoinhibited to membrane-embedded molecular states. We further discuss the formation and maturation of membrane pores formed by BAX/BAK/BOK, GSDMs and MLKL, leading to diverse pore architectures. Lastly, we highlight commonalities and differences of PFP mechanisms involving BAX/BAK/BOK, GSDMs and MLKL and conclude with a discussion on how, in a population of challenged cells, the coexistence of cell death modalities may have profound physiological and pathophysiological implications., (© 2022. Springer Nature Limited.)
- Published
- 2023
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13. Unexpected complexity of the ammonia monooxygenase in archaea.
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Hodgskiss LH, Melcher M, Kerou M, Chen W, Ponce-Toledo RI, Savvides SN, Wienkoop S, Hartl M, and Schleper C
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- Nitrification, Native Polyacrylamide Gel Electrophoresis, Phylogeny, Gene Expression, Archaea classification, Archaea enzymology, Oxidoreductases chemistry, Oxidoreductases genetics, Oxidoreductases metabolism
- Abstract
Ammonia oxidation, as the first step of nitrification, constitutes a critical process in the global nitrogen cycle. However, fundamental knowledge of its key enzyme, the copper-dependent ammonia monooxygenase, is lacking, in particular for the environmentally abundant ammonia-oxidizing archaea (AOA). Here the structure of the enzyme is investigated by blue-native gel electrophoresis and proteomics from native membrane complexes of two AOA. Besides the known AmoABC subunits and the earlier predicted AmoX, two new protein subunits, AmoY and AmoZ, were identified. They are unique to AOA, highly conserved and co-regulated, and their genes are linked to other AMO subunit genes in streamlined AOA genomes. Modeling and in-gel cross-link approaches support an overall protomer structure similar to the distantly related bacterial particulate methane monooxygenase but also reveals clear differences in extracellular domains of the enzyme. These data open avenues for further structure-function studies of this ecologically important nitrification complex., (© 2023. The Author(s).)
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- 2023
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14. Mechanism of receptor assembly via the pleiotropic adipokine Leptin.
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Tsirigotaki A, Dansercoer A, Verschueren KHG, Marković I, Pollmann C, Hafer M, Felix J, Birck C, Van Putte W, Catteeuw D, Tavernier J, Fernando Bazan J, Piehler J, Savvides SN, and Verstraete K
- Subjects
- Protein Isoforms genetics, Signal Transduction, Leptin genetics, Leptin metabolism, Leptin pharmacology, Adipokines
- Abstract
The adipokine Leptin activates its receptor LEP-R in the hypothalamus to regulate body weight and exerts additional pleiotropic functions in immunity, fertility and cancer. However, the structure and mechanism of Leptin-mediated LEP-R assemblies has remained unclear. Intriguingly, the signaling-competent isoform of LEP-R is only lowly abundant amid several inactive short LEP-R isoforms contributing to a mechanistic conundrum. Here we show by X-ray crystallography and cryo-EM that, in contrast to long-standing paradigms, Leptin induces type I cytokine receptor assemblies featuring 3:3 stoichiometry and demonstrate such Leptin-induced trimerization of LEP-R on living cells via single-molecule microscopy. In mediating these assemblies, Leptin undergoes drastic restructuring that activates its site III for binding to the Ig domain of an adjacent LEP-R. These interactions are abolished by mutations linked to obesity. Collectively, our study provides the structural and mechanistic framework for how evolutionarily conserved Leptin:LEP-R assemblies with 3:3 stoichiometry can engage distinct LEP-R isoforms to achieve signaling., (© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.)
- Published
- 2023
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15. EGOC inhibits TOROID polymerization by structurally activating TORC1.
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Prouteau M, Bourgoint C, Felix J, Bonadei L, Sadian Y, Gabus C, Savvides SN, Gutsche I, Desfosses A, and Loewith R
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- Mechanistic Target of Rapamycin Complex 1 chemistry, Mechanistic Target of Rapamycin Complex 1 metabolism, Polymerization, Transcription Factors metabolism, Saccharomyces cerevisiae metabolism, Glucose metabolism, Saccharomyces cerevisiae Proteins metabolism
- Abstract
Target of rapamycin complex 1 (TORC1) is a protein kinase controlling cell homeostasis and growth in response to nutrients and stresses. In Saccharomyces cerevisiae, glucose depletion triggers a redistribution of TORC1 from a dispersed localization over the vacuole surface into a large, inactive condensate called TOROID (TORC1 organized in inhibited domains). However, the mechanisms governing this transition have been unclear. Here, we show that acute depletion and repletion of EGO complex (EGOC) activity is sufficient to control TOROID distribution, independently of other nutrient-signaling pathways. The 3.9-Å-resolution structure of TORC1 from TOROID cryo-EM data together with interrogation of key interactions in vivo provide structural insights into TORC1-TORC1' and TORC1-EGOC interaction interfaces. These data support a model in which glucose-dependent activation of EGOC triggers binding to TORC1 at an interface required for TOROID assembly, preventing TORC1 polymerization and promoting release of active TORC1., (© 2023. The Author(s).)
- Published
- 2023
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16. Structural basis of activation and antagonism of receptor signaling mediated by interleukin-27.
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Składanowska K, Bloch Y, Strand J, White KF, Hua J, Aldridge D, Welin M, Logan DT, Soete A, Merceron R, Murphy C, Provost M, Bazan JF, Hunter CA, Hill JA, and Savvides SN
- Subjects
- Humans, Mice, Animals, Cytokine Receptor gp130 metabolism, Receptors, Cytokine metabolism, Interleukin-12, Cytokines, Antibodies, Monoclonal pharmacology, Epitopes, Interleukin-23, Interleukin-27
- Abstract
Interleukin-27 (IL-27) uniquely assembles p28 and EBI3 subunits to a heterodimeric cytokine that signals via IL-27Rα and gp130. To provide the structural framework for receptor activation by IL-27 and its emerging therapeutic targeting, we report here crystal structures of mouse IL-27 in complex with IL-27Rα and of human IL-27 in complex with SRF388, a monoclonal antibody undergoing clinical trials with oncology indications. One face of the helical p28 subunit interacts with EBI3, while the opposite face nestles into the interdomain elbow of IL-27Rα to juxtapose IL-27Rα to EBI3. This orients IL-27Rα for paired signaling with gp130, which only uses its immunoglobulin domain to bind to IL-27. Such a signaling complex is distinct from those mediated by IL-12 and IL-23. The SRF388 binding epitope on IL-27 overlaps with the IL-27Rα interaction site explaining its potent antagonistic properties. Collectively, our findings will facilitate the mechanistic interrogation, engineering, and therapeutic targeting of IL-27., Competing Interests: Declaration of interests J.S., K.F.W., and J.A.H are former or current employees and stockholders of Surface Oncology. C.A.H. is a member of the scientific advisory board of Surface Oncology. J.S., K.F.W., and J.H. are listed as co-inventors on granted patent US11332524B2 relating to certain findings reported in this manuscript., (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.)
- Published
- 2022
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17. The Fab region of IgG impairs the internalization pathway of FcRn upon Fc engagement.
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Brinkhaus M, Pannecoucke E, van der Kooi EJ, Bentlage AEH, Derksen NIL, Andries J, Balbino B, Sips M, Ulrichts P, Verheesen P, de Haard H, Rispens T, Savvides SN, and Vidarsson G
- Subjects
- Animals, Histocompatibility Antigens Class I, Immunoglobulin Fc Fragments chemistry, Immunoglobulin G, Macaca fascicularis metabolism, Protein Binding, Receptors, Fc, Antibodies, Monoclonal, Autoimmune Diseases drug therapy
- Abstract
Binding to the neonatal Fc receptor (FcRn) extends serum half-life of IgG, and antagonizing this interaction is a promising therapeutic approach in IgG-mediated autoimmune diseases. Fc-MST-HN, designed for enhanced FcRn binding capacity, has not been evaluated in the context of a full-length antibody, and the structural properties of the attached Fab regions might affect the FcRn-mediated intracellular trafficking pathway. Here we present a comprehensive comparative analysis of the IgG salvage pathway between two full-size IgG1 variants, containing wild type and MST-HN Fc fragments, and their Fc-only counterparts. We find no evidence of Fab-regions affecting FcRn binding in cell-free assays, however, cellular assays show impaired binding of full-size IgG to FcRn, which translates into improved intracellular FcRn occupancy and intracellular accumulation of Fc-MST-HN compared to full size IgG1-MST-HN. The crystal structure of Fc-MST-HN in complex with FcRn provides a plausible explanation why the Fab disrupts the interaction only in the context of membrane-associated FcRn. Importantly, we find that Fc-MST-HN outperforms full-size IgG1-MST-HN in reducing IgG levels in cynomolgus monkeys. Collectively, our findings identify the cellular membrane context as a critical factor in FcRn biology and therapeutic targeting., (© 2022. The Author(s).)
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- 2022
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18. The Charcot-Leyden crystal protein galectin-10 is not a major determinant of human regulatory T-cell function.
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Arroyo-Hornero R, Aegerter H, Hamad I, Corte-Real B, Staes K, van der Woning B, Verstraete K, Savvides SN, Lambrecht BN, and Kleinewietfeld M
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- Eosinophils metabolism, Galectins metabolism, Glycoproteins metabolism, Humans, Lysophospholipase chemistry, Lysophospholipase metabolism, T-Lymphocytes, Regulatory metabolism
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- 2022
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19. Structural basis of human IL-18 sequestration by the decoy receptor IL-18 binding protein in inflammation and tumor immunity.
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Detry S, Andries J, Bloch Y, Gabay C, Clancy DM, and Savvides SN
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- COVID-19 immunology, Humans, Inflammation, Neoplasms immunology, Intercellular Signaling Peptides and Proteins, Interleukin-18 metabolism
- Abstract
Human Interleukin-18 (IL-18) is an omnipresent proinflammatory cytokine of the IL-1 family with central roles in autoimmune and inflammatory diseases and serves as a staple biomarker in the evaluation of inflammation in physiology and disease, including the inflammatory phase of COVID-19. The sequestration of IL-18 by its soluble decoy receptor IL-18-Binding Protein (IL-18BP) is critical to the regulation of IL-18 activity. Since an imbalance in expression and circulating levels of IL-18 is associated with disease, structural insights into how IL-18BP outcompetes binding of IL-18 by its cognate cell-surface receptors are highly desirable; however, the structure of human IL-18BP in complex with IL-18 has been elusive. Here, we elucidate the sequestration mechanism of human IL-18 mediated by IL-18BP based on the crystal structure of the IL-18:IL-18BP complex. These detailed structural snapshots reveal the interaction landscape leading to the ultra-high affinity of IL-18BP toward IL-18 and identify substantial differences with respect to previously characterized complexes of IL-18 with IL-18BP of viral origin. Furthermore, our structure captured a fortuitous higher-order assembly between IL-18 and IL-18BP coordinated by a disulfide-bond distal to the binding surface connecting IL-18 and IL-18BP molecules from different complexes, resulting in a novel tetramer with 2:2 stoichiometry. This tetrapartite assembly was found to restrain IL-18 activity more effectively than the canonical 1:1 complex. Collectively, our findings provide a framework for innovative, structure-driven therapeutic strategies and further functional interrogation of IL-18 in physiology and disease., Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2022
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20. Design of protein-binding proteins from the target structure alone.
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Cao L, Coventry B, Goreshnik I, Huang B, Sheffler W, Park JS, Jude KM, Marković I, Kadam RU, Verschueren KHG, Verstraete K, Walsh STR, Bennett N, Phal A, Yang A, Kozodoy L, DeWitt M, Picton L, Miller L, Strauch EM, DeBouver ND, Pires A, Bera AK, Halabiya S, Hammerson B, Yang W, Bernard S, Stewart L, Wilson IA, Ruohola-Baker H, Schlessinger J, Lee S, Savvides SN, Garcia KC, and Baker D
- Subjects
- Amino Acids metabolism, Binding Sites, Protein Binding, Carrier Proteins metabolism, Proteins chemistry
- Abstract
The design of proteins that bind to a specific site on the surface of a target protein using no information other than the three-dimensional structure of the target remains a challenge
1-5 . Here we describe a general solution to this problem that starts with a broad exploration of the vast space of possible binding modes to a selected region of a protein surface, and then intensifies the search in the vicinity of the most promising binding modes. We demonstrate the broad applicability of this approach through the de novo design of binding proteins to 12 diverse protein targets with different shapes and surface properties. Biophysical characterization shows that the binders, which are all smaller than 65 amino acids, are hyperstable and, following experimental optimization, bind their targets with nanomolar to picomolar affinities. We succeeded in solving crystal structures of five of the binder-target complexes, and all five closely match the corresponding computational design models. Experimental data on nearly half a million computational designs and hundreds of thousands of point mutants provide detailed feedback on the strengths and limitations of the method and of our current understanding of protein-protein interactions, and should guide improvements of both. Our approach enables the targeted design of binders to sites of interest on a wide variety of proteins for therapeutic and diagnostic applications., (© 2022. This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.)- Published
- 2022
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21. Point mutation I634A in the glucocorticoid receptor causes embryonic lethality by reduced ligand binding.
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Timmermans S, Verhoog NJD, Van Looveren K, Dewaele S, Hochepied T, Eggermont M, Gilbert B, Boerema-de Munck A, Vanderhaeghen T, Vanden Berghe J, Garcia Gonzalez N, Vandewalle J, Bloch Y, Provost M, Savvides SN, De Bosscher K, Declercq W, Rottier RJ, Louw A, and Libert C
- Subjects
- Animals, Glucocorticoids pharmacology, Ligands, Mice, Dexamethasone pharmacology, Point Mutation, Receptors, Glucocorticoid genetics, Receptors, Glucocorticoid metabolism
- Abstract
The glucocorticoid (GC) receptor (GR) is essential for normal development and in the initiation of inflammation. Healthy GR
dim/dim mice with reduced dimerization propensity due to a point mutation (A465T) at the dimer interface of the GR DNA-binding domain (DBD) (here GRD/D ) have previously helped to define the functions of GR monomers and dimers. Since GRD/D retains residual dimerization capacity, here we generated the dimer-nullifying double mutant GRD+L/D+L mice, featuring an additional mutation (I634A) in the ligand-binding domain (LBD) of GR. These mice are perinatally lethal, as are GRL/L mice (these mice have the I634A mutation but not the A465T mutation), displaying improper lung and skin formation. Using embryonic fibroblasts, high and low doses of dexamethasone (Dex), nuclear translocation assays, RNAseq, dimerization assays, and ligand-binding assays (and Kd values), we found that the lethal phenotype in these mice is due to insufficient ligand binding. These data suggest there is some correlation between GR dimerization potential and ligand affinity. We conclude that even a mutation as subtle as I634A, at a position not directly involved in ligand interactions sensu stricto, can still influence ligand binding and have a lethal outcome., Competing Interests: Conflict of interest The authors declare that they have no conflict of interest with the contents of this article., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)- Published
- 2022
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22. Hapln1b, a central organizer of the ECM, modulates kit signaling to control developmental hematopoiesis in zebrafish.
- Author
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Mahony CB, Cacialli P, Pasche C, Monteiro R, Savvides SN, and Bertrand JY
- Subjects
- Animals, Extracellular Matrix, Hematopoietic Stem Cells, Zebrafish Proteins genetics, Hematopoiesis, Zebrafish
- Abstract
During early vertebrate development, hematopoietic stem and progenitor cells (HSPCs) are produced in hemogenic endothelium located in the dorsal aorta, before they migrate to a transient niche where they expand to the fetal liver and the caudal hematopoietic tissue, in mammals and zebrafish, respectively. In zebrafish, previous studies have shown that the extracellular matrix (ECM) around the aorta must be degraded to enable HSPCs to leave the aortic floor and reach blood circulation. However, the role of the ECM components in HSPC specification has never been addressed. In this study, hapln1b, a key component of the ECM, was specifically expressed in hematopoietic sites in the zebrafish embryo. Gain- and loss-of-function experiments all resulted in the absence of HSPCs in the early embryo, showing that hapln1b is necessary, at the correct level, to specify HSPCs in the hemogenic endothelium. Furthermore, the expression of hapln1b was necessary to maintain the integrity of the ECM through its link domain. By combining functional analyses and computer modeling, we showed that kitlgb interacts with the ECM to specify HSPCs. The findings show that the ECM is an integral component of the microenvironment and mediates the cytokine signaling that is necessary for HSPC specification., (© 2021 by The American Society of Hematology. Licensed under Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0), permitting only noncommercial, nonderivative use with attribution. All other rights reserved.)
- Published
- 2021
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23. Structure-aided optimization of non-nucleoside M. tuberculosis thymidylate kinase inhibitors.
- Author
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Song L, Merceron R, Hulpia F, Lucía A, Gracia B, Jian Y, Risseeuw MDP, Verstraelen T, Cos P, Aínsa JA, Boshoff HI, Munier-Lehmann H, Savvides SN, and Van Calenbergh S
- Subjects
- Antitubercular Agents chemical synthesis, Antitubercular Agents chemistry, Dose-Response Relationship, Drug, Enzyme Inhibitors chemical synthesis, Enzyme Inhibitors chemistry, Microbial Sensitivity Tests, Molecular Structure, Mycobacterium tuberculosis enzymology, Nucleoside-Phosphate Kinase metabolism, Piperidines chemical synthesis, Piperidines chemistry, Structure-Activity Relationship, Thymine chemical synthesis, Thymine chemistry, Antitubercular Agents pharmacology, Enzyme Inhibitors pharmacology, Mycobacterium tuberculosis drug effects, Nucleoside-Phosphate Kinase antagonists & inhibitors, Piperidines pharmacology, Thymine pharmacology
- Abstract
Mycobacterium tuberculosis thymidylate kinase (MtTMPK) has emerged as an attractive target for rational drug design. We recently investigated new families of non-nucleoside MtTMPK inhibitors in an effort to diversify MtTMPK inhibitor chemical space. We here report a new series of MtTMPK inhibitors by combining the Topliss scheme with rational drug design approaches, fueled by two co-crystal structures of MtTMPK in complex with developed inhibitors. These efforts furnished the most potent MtTMPK inhibitors in our assay, with two analogues displaying low micromolar MIC values against H37Rv Mtb. Prepared inhibitors address new sub-sites in the MtTMPK nucleotide binding pocket, thereby offering new insights into its druggability. We studied the role of efflux pumps as well as the impact of cell wall permeabilizers for selected compounds to potentially provide an explanation for the lack of correlation between potent enzyme inhibition and whole-cell activity., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier Masson SAS. All rights reserved.)
- Published
- 2021
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24. Structural basis of cytokine-mediated activation of ALK family receptors.
- Author
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De Munck S, Provost M, Kurikawa M, Omori I, Mukohyama J, Felix J, Bloch Y, Abdel-Wahab O, Bazan JF, Yoshimi A, and Savvides SN
- Subjects
- Anaplastic Lymphoma Kinase classification, Anaplastic Lymphoma Kinase genetics, Binding Sites, Enzyme Activation, Epidermal Growth Factor chemistry, Glycine, HEK293 Cells, Humans, Models, Molecular, Multiprotein Complexes chemistry, Multiprotein Complexes metabolism, Mutation, Protein Binding, Protein Domains, Protein Multimerization, Substrate Specificity, Anaplastic Lymphoma Kinase chemistry, Anaplastic Lymphoma Kinase metabolism, Cytokines chemistry, Cytokines metabolism, Receptor Protein-Tyrosine Kinases chemistry, Receptor Protein-Tyrosine Kinases metabolism
- Abstract
Anaplastic lymphoma kinase (ALK)
1 and the related leukocyte tyrosine kinase (LTK)2 are recently deorphanized receptor tyrosine kinases3 . Together with their activating cytokines, ALKAL1 and ALKAL24-6 (also called FAM150A and FAM150B or AUGβ and AUGα, respectively), they are involved in neural development7 , cancer7-9 and autoimmune diseases10 . Furthermore, mammalian ALK recently emerged as a key regulator of energy expenditure and weight gain11 , consistent with a metabolic role for Drosophila ALK12 . Despite such functional pleiotropy and growing therapeutic relevance13,14 , structural insights into ALK and LTK and their complexes with cognate cytokines have remained scarce. Here we show that the cytokine-binding segments of human ALK and LTK comprise a novel architectural chimera of a permuted TNF-like module that braces a glycine-rich subdomain featuring a hexagonal lattice of long polyglycine type II helices. The cognate cytokines ALKAL1 and ALKAL2 are monomeric three-helix bundles, yet their binding to ALK and LTK elicits similar dimeric assemblies with two-fold symmetry, that tent a single cytokine molecule proximal to the cell membrane. We show that the membrane-proximal EGF-like domain dictates the apparent cytokine preference of ALK. Assisted by these diverse structure-function findings, we propose a structural and mechanistic blueprint for complexes of ALK family receptors, and thereby extend the repertoire of ligand-mediated dimerization mechanisms adopted by receptor tyrosine kinases., (© 2021. The Author(s), under exclusive licence to Springer Nature Limited.)- Published
- 2021
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25. CRISPR-SID: Identifying EZH2 as a druggable target for desmoid tumors via in vivo dependency mapping.
- Author
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Naert T, Tulkens D, Van Nieuwenhuysen T, Przybyl J, Demuynck S, van de Rijn M, Al-Jazrawe M, Alman BA, Coucke PJ, De Leeneer K, Vanhove C, Savvides SN, Creytens D, and Vleminckx K
- Subjects
- Abdominal Neoplasms genetics, Adenomatous Polyposis Coli genetics, Animals, Carcinogenesis genetics, Cell Line, Tumor, Cyclic AMP Response Element-Binding Protein, Fibromatosis, Aggressive genetics, Gene Expression Regulation, Neoplastic, Humans, Neoplasm Proteins genetics, Neoplasm Proteins metabolism, Nerve Tissue Proteins, Oncogenes, Polycomb Repressive Complex 2 metabolism, Transcription Factors genetics, Transcription Factors metabolism, Wnt Signaling Pathway, Xenopus, beta Catenin, CRISPR-Cas Systems, Clustered Regularly Interspaced Short Palindromic Repeats, Enhancer of Zeste Homolog 2 Protein genetics, Enhancer of Zeste Homolog 2 Protein isolation & purification, Enhancer of Zeste Homolog 2 Protein metabolism, Gene Editing methods
- Abstract
Cancer precision medicine implies identification of tumor-specific vulnerabilities associated with defined oncogenic pathways. Desmoid tumors are soft-tissue neoplasms strictly driven by Wnt signaling network hyperactivation. Despite this clearly defined genetic etiology and the strict and unique implication of the Wnt/β-catenin pathway, no specific molecular targets for these tumors have been identified. To address this caveat, we developed fast, efficient, and penetrant genetic Xenopus tropicalis desmoid tumor models to identify and characterize drug targets. We used multiplexed CRISPR/Cas9 genome editing in these models to simultaneously target a tumor suppressor gene ( apc ) and candidate dependency genes. Our methodology CRISPR/Cas9 selection-mediated identification of dependencies (CRISPR-SID) uses calculated deviations between experimentally observed gene editing outcomes and deep-learning-predicted double-strand break repair patterns to identify genes under negative selection during tumorigenesis. This revealed EZH2 and SUZ12 , both encoding polycomb repressive complex 2 components, and the transcription factor CREB3L1 as genetic dependencies for desmoid tumors. In vivo EZH2 inhibition by Tazemetostat induced partial regression of established autochthonous tumors. In vitro models of patient desmoid tumor cells revealed a direct effect of Tazemetostat on Wnt pathway activity. CRISPR-SID represents a potent approach for in vivo mapping of tumor vulnerabilities and drug target identification., Competing Interests: The authors declare no competing interest.
- Published
- 2021
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26. A recombinant antibody fragment directed to the thymic stromal lymphopoietin receptor (CRLF2) efficiently targets pediatric Philadelphia chromosome-like acute lymphoblastic leukemia.
- Author
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Mohamed SMA, Wohlmann A, Schofield P, Sia KCS, McCalmont H, Savvides SN, Verstraete K, Kavallaris M, Christ D, Friedrich KH, Bayat N, and Lock RB
- Subjects
- Animals, Cell Line, Tumor, Child, Endocytosis, HEK293 Cells, Humans, Mice, Phosphorylation, STAT5 Transcription Factor metabolism, Signal Transduction, Single-Chain Antibodies isolation & purification, Immunoglobulin Fragments metabolism, Philadelphia Chromosome, Precursor Cell Lymphoblastic Leukemia-Lymphoma pathology, Receptors, Cytokine metabolism, Recombinant Proteins metabolism
- Abstract
Antibody fragments are promising building blocks for developing targeted therapeutics, thus improving treatment efficacy while minimising off-target toxicity. Despite recent advances in targeted therapeutics, patients with Philadelphia-like acute lymphoblastic leukemia (Ph-like ALL), a high-risk malignancy, lack specific and effective targeted treatments. Cytokine receptor-like factor 2 (CRLF2) is overexpressed in 50% of Ph-like ALL cases, conferring the survival of leukemia blasts through activation of the JAK/STAT signalling pathway. Targeting such a vital cell-surface protein could result in potent anti-leukaemic efficacy and reduce the likelihood of relapse associated with antigen loss. Herein, we developed a novel single-chain variable fragment (scFv) against CRLF2 based on a monoclonal antibody raised against the recombinant extracellular domain of human TSLPRα chain. The scFv fragment demonstrated excellent binding affinity with CRLF2 protein in the nanomolar range. Cellular association studies in vitro using an inducible CRLF2 knockdown cell line and ex vivo using patient-derived xenografts revealed the selective association of the scFv with CRLF2. The fragment exhibited significant receptor antagonistic effects on STAT5 signalling, suggesting possible therapeutic implications in vivo. This study is the first to describe the potential use of a novel scFv for targeting Ph-like ALL., (Copyright © 2021 Elsevier B.V. All rights reserved.)
- Published
- 2021
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27. Charcot-Leyden crystals and other protein crystals driving type 2 immunity and allergy.
- Author
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Aegerter H, Smole U, Heyndrickx I, Verstraete K, Savvides SN, Hammad H, and Lambrecht BN
- Subjects
- Animals, Biomarkers, Crystallins immunology, Disease Susceptibility, Humans, Hypersensitivity metabolism, Inflammation Mediators metabolism, Mice, Organ Specificity immunology, Proteins chemistry, Allergens immunology, Hypersensitivity etiology, Immunity, Proteins immunology
- Abstract
Protein crystals derived from innate immune cells have been synonymous with a Type-2 immune response in both mouse and man for over 150 years. Eosinophilic Galectin-10 (Charcot-Leyden) crystals in humans, and Ym1/Ym2 crystals in mice are frequently found in the context of parasitic infections, but also in diseases such as asthma and chronic rhinosinusitis. Despite their notable presence, these crystals are often overlooked as trivial markers of Type-2 inflammation. Here, we discuss the source, context, and role of protein crystallization. We focus on similarities observed between Galectin-10 and Ym1/2 crystals in driving immune responses; the subsequent benefit to the host during worm infection, and conversely the detrimental exacerbation of inflammation and mucus production during asthma., (Copyright © 2021. Published by Elsevier Ltd.)
- Published
- 2021
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28. Minimal epitope for Mannitou IgM on paucimannose-carrying glycoproteins.
- Author
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Robakiewicz S, Bridot C, Serna S, Gimeno A, Echeverria B, Delgado S, de Ruyck J, Semwal S, Charro D, Dansercoer A, Verstraete K, Azkargorta M, van Noort K, Wilbers RHP, Savvides SN, Abrescia NGA, Arda A, Reichardt NC, Jiménez-Barbero J, and Bouckaert J
- Subjects
- Animals, DNA-Binding Proteins, Epitopes chemistry, Fucose metabolism, Humans, Immunoglobulin M, Mammals metabolism, Membrane Proteins, Mice, Polysaccharides chemistry, Glycoproteins metabolism, Schistosoma mansoni chemistry, Schistosoma mansoni metabolism
- Abstract
Paucimannosidic glycans are restricted to the core structure [Man1-3GlcNAc2Fuc0-1] of N-glycans and are rarely found in mammalian tissues. Yet, especially [Man2-3GlcNAc2Fuc1] have been found significantly upregulated in tumors, including in colorectal and liver cancer. Mannitou IgM is a murine monoclonal antibody that was previously shown to recognize Man3GlcNAc2 with an almost exclusive selectivity. Here, we have sought the definition of the minimal glycan epitope of Mannitou IgM, initiated by screening on a newly designed paucimannosidic glycan microarray; among the best binders were Man3GlcNAc2 and its α1,6 core-fucosylated variant, Man3GlcNAc2Fuc1. Unexpectedly and in contrast to earlier findings, Man5GlcNAc2-type structures bind equally well and a large tolerance was observed for substitutions on the α1,6 arm. It was confirmed that any substitution on the single α1,3-linked mannose completely abolishes binding. Surface plasmon resonance for kinetic measurements of Mannitou IgM binding, either directly on the glycans or as presented on omega-1 and kappa-5 soluble egg antigens from the helminth parasite Schistosoma mansoni, showed submicromolar affinities. To characterize the epitope in greater and atomic detail, saturation transfer difference nuclear magnetic resonance spectroscopy was performed with the Mannitou antigen-binding fragment. The STD-NMR data demonstrated the strongest interactions with the aliphatic protons H1 and H2 of the α1-3-linked mannose and weaker imprints on its H3, H4 and H5 protons. In conclusion, Mannitou IgM binding requires a nonsubstituted α1,3-linked mannose branch of paucimannose also on proteins, making it a highly specific tool for the distinction of concurrent human tumor-associated carbohydrate antigens., (© The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2021
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29. Acetyl-CoA is produced by the citrate synthase homology module of ATP-citrate lyase.
- Author
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Verstraete K, Verschueren KHG, Dansercoer A, and Savvides SN
- Subjects
- Acetyl Coenzyme A, Citrate (si)-Synthase, Multienzyme Complexes, Oxo-Acid-Lyases, ATP Citrate (pro-S)-Lyase genetics, Adenosine Triphosphate
- Published
- 2021
- Full Text
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30. Distinct EH domains of the endocytic TPLATE complex confer lipid and protein binding.
- Author
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Yperman K, Papageorgiou AC, Merceron R, De Munck S, Bloch Y, Eeckhout D, Jiang Q, Tack P, Grigoryan R, Evangelidis T, Van Leene J, Vincze L, Vandenabeele P, Vanhaecke F, Potocký M, De Jaeger G, Savvides SN, Tripsianes K, Pleskot R, and Van Damme D
- Subjects
- Adaptor Proteins, Signal Transducing genetics, Arabidopsis Proteins, Calcium-Binding Proteins genetics, Cell Membrane metabolism, Crystallography, X-Ray, Membrane Proteins chemistry, Molecular Dynamics Simulation, Plant Proteins genetics, Plants, Genetically Modified, Protein Domains, Protein Transport, Sequence Alignment, Nicotiana genetics, Adaptor Proteins, Signal Transducing chemistry, Calcium-Binding Proteins chemistry, Endocytosis, Plant Proteins chemistry, Protein Binding
- Abstract
Clathrin-mediated endocytosis (CME) is the gatekeeper of the plasma membrane. In contrast to animals and yeasts, CME in plants depends on the TPLATE complex (TPC), an evolutionary ancient adaptor complex. However, the mechanistic contribution of the individual TPC subunits to plant CME remains elusive. In this study, we used a multidisciplinary approach to elucidate the structural and functional roles of the evolutionary conserved N-terminal Eps15 homology (EH) domains of the TPC subunit AtEH1/Pan1. By integrating high-resolution structural information obtained by X-ray crystallography and NMR spectroscopy with all-atom molecular dynamics simulations, we provide structural insight into the function of both EH domains. Both domains bind phosphatidic acid with a different strength, and only the second domain binds phosphatidylinositol 4,5-bisphosphate. Unbiased peptidome profiling by mass-spectrometry revealed that the first EH domain preferentially interacts with the double N-terminal NPF motif of a previously unidentified TPC interactor, the integral membrane protein Secretory Carrier Membrane Protein 5 (SCAMP5). Furthermore, we show that AtEH/Pan1 proteins control the internalization of SCAMP5 via this double NPF peptide interaction motif. Collectively, our structural and functional studies reveal distinct but complementary roles of the EH domains of AtEH/Pan1 in plant CME and connect the internalization of SCAMP5 to the TPLATE complex.
- Published
- 2021
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31. Alzheimer's-causing mutations shift Aβ length by destabilizing γ-secretase-Aβn interactions.
- Author
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Szaruga M, Munteanu B, Lismont S, Veugelen S, Horré K, Mercken M, Saido TC, Ryan NS, De Vos T, Savvides SN, Gallardo R, Schymkowitz J, Rousseau F, Fox NC, Hopf C, De Strooper B, and Chávez-Gutiérrez L
- Published
- 2021
- Full Text
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32. Engineering and crystal structure of a monomeric FLT3 ligand variant.
- Author
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Pannecoucke E, Raes L, and Savvides SN
- Subjects
- Amino Acid Sequence, HEK293 Cells, Humans, Membrane Proteins chemistry, Membrane Proteins metabolism, Protein Binding physiology, Protein Structure, Secondary, Protein Structure, Tertiary, fms-Like Tyrosine Kinase 3 chemistry, fms-Like Tyrosine Kinase 3 metabolism, Genetic Variation genetics, Membrane Proteins genetics, Protein Engineering methods, X-Ray Diffraction methods, fms-Like Tyrosine Kinase 3 genetics
- Abstract
The overarching paradigm for the activation of class III and V receptor tyrosine kinases (RTKs) prescribes cytokine-mediated dimerization of the receptor ectodomains and homotypic receptor-receptor interactions. However, structural studies have shown that the hematopoietic receptor FLT3, a class III RTK, does not appear to engage in such receptor-receptor contacts, despite its efficient dimerization by dimeric FLT3 ligand (FL). As part of efforts to better understand the intricacies of FLT3 activation, we sought to engineer a monomeric FL. It was found that a Leu27Asp substitution at the dimer interface of the cytokine led to a stable monomeric cytokine (FL
L27D ) without abrogation of receptor binding. The crystal structure of FLL27D at 1.65 Å resolution revealed that the introduced point mutation led to shielding of the hydrophobic footprint of the dimerization interface in wild-type FL without affecting the conformation of the FLT3 binding site. Thus, FLL27D can serve as a monomeric FL variant to further interrogate the assembly mechanism of extracellular complexes of FLT3 in physiology and disease., (open access.)- Published
- 2021
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33. Cell-penetrating Alphabody protein scaffolds for intracellular drug targeting.
- Author
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Pannecoucke E, Van Trimpont M, Desmet J, Pieters T, Reunes L, Demoen L, Vuylsteke M, Loverix S, Vandenbroucke K, Alard P, Henderikx P, Deroo S, Baatz F, Lorent E, Thiolloy S, Somers K, McGrath Y, Van Vlierberghe P, Lasters I, and Savvides SN
- Subjects
- Animals, Apoptosis, Cell Line, Cell Line, Tumor, Drug Delivery Systems, Humans, Mice, Myeloid Cell Leukemia Sequence 1 Protein metabolism, Neoplasms, Peptides chemistry
- Abstract
The therapeutic scope of antibody and nonantibody protein scaffolds is still prohibitively limited against intracellular drug targets. Here, we demonstrate that the Alphabody scaffold can be engineered into a cell-penetrating protein antagonist against induced myeloid leukemia cell differentiation protein MCL-1, an intracellular target in cancer, by grafting the critical B-cell lymphoma 2 homology 3 helix of MCL-1 onto the Alphabody and tagging the scaffold's termini with designed cell-penetration polypeptides. Introduction of an albumin-binding moiety extended the serum half-life of the engineered Alphabody to therapeutically relevant levels, and administration thereof in mouse tumor xenografts based on myeloma cell lines reduced tumor burden. Crystal structures of such a designed Alphabody in complex with MCL-1 and serum albumin provided the structural blueprint of the applied design principles. Collectively, we provide proof of concept for the use of Alphabodies against intracellular disease mediators, which, to date, have remained in the realm of small-molecule therapeutics., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).)
- Published
- 2021
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34. Molecular architecture of the endocytic TPLATE complex.
- Author
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Yperman K, Wang J, Eeckhout D, Winkler J, Vu LD, Vandorpe M, Grones P, Mylle E, Kraus M, Merceron R, Nolf J, Mor E, De Bruyn P, Loris R, Potocký M, Savvides SN, De Rybel B, De Jaeger G, Van Damme D, and Pleskot R
- Abstract
Eukaryotic cells rely on endocytosis to regulate their plasma membrane proteome and lipidome. Most eukaryotic groups, except fungi and animals, have retained the evolutionary ancient TSET complex as an endocytic regulator. Unlike other coatomer complexes, structural insight into TSET is lacking. Here, we reveal the molecular architecture of plant TSET [TPLATE complex (TPC)] using an integrative structural approach. We identify crucial roles for specific TSET subunits in complex assembly and membrane interaction. Our data therefore generate fresh insight into the differences between the hexameric TSET in Dictyostelium and the octameric TPC in plants. Structural elucidation of this ancient adaptor complex represents the missing piece in the coatomer puzzle and vastly advances our functional as well as evolutionary insight into the process of endocytosis., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).)
- Published
- 2021
- Full Text
- View/download PDF
35. Smoking cessation avatar-led Acceptance and Commitment Therapy digital intervention: feasibility and acceptability in young adults.
- Author
-
Karekla M and Savvides SN
- Subjects
- Adolescent, Adult, Feasibility Studies, Female, Humans, Male, Smokers, Smoking, Young Adult, Acceptance and Commitment Therapy, Smoking Cessation
- Abstract
Smoking remains a global concern especially among youth and smoking cessation interventions have not been particularly successful with this age group. The aim of the present study was to evaluate the feasibility and acceptability of an innovative avatar-led, digital intervention grounded in Acceptance and Commitment Therapy (ACT) for smoking cessation in youth. Participants were 49 university student smokers, aged 18-28 years old (Mage = 22.50, SD = 2.56; 64.3% females). Participants found the program satisfactory, useful, and motivating. Participants enjoyed the digitally unique components of the intervention, such as videos, metaphors, and games, more than the overall graphics and the appearance of the avatars. Results of this study are encouraging for the acceptability and satisfaction with avatar-led digitized ACT interventions for smoking cessation targeting young smokers. Participants suggested that future program advances should include a more reality-based user experience and more interactive avatars. Future adaptations should consider additional ways to decrease attrition rates and further increase satisfaction and motivation to complete the program and quit smoking., (© Society of Behavioral Medicine 2019. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2021
- Full Text
- View/download PDF
36. Attenuated CSF-1R signalling drives cerebrovascular pathology.
- Author
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Delaney C, Farrell M, Doherty CP, Brennan K, O'Keeffe E, Greene C, Byrne K, Kelly E, Birmingham N, Hickey P, Cronin S, Savvides SN, Doyle SL, and Campbell M
- Subjects
- Adult, Brain, Humans, Microglia, Neuroglia, Receptors, Granulocyte-Macrophage Colony-Stimulating Factor, Leukoencephalopathies, Signal Transduction
- Abstract
Cerebrovascular pathologies occur in up to 80% of cases of Alzheimer's disease; however, the underlying mechanisms that lead to perivascular pathology and accompanying blood-brain barrier (BBB) disruption are still not fully understood. We have identified previously unreported mutations in colony stimulating factor-1 receptor (CSF-1R) in an ultra-rare autosomal dominant condition termed adult-onset leucoencephalopathy with axonal spheroids and pigmented glia (ALSP). Cerebrovascular pathologies such as cerebral amyloid angiopathy (CAA) and perivascular p-Tau were some of the primary neuropathological features of this condition. We have identified two families with different dominant acting alleles with variants located in the kinase region of the CSF-1R gene, which confer a lack of kinase activity and signalling. The protein product of this gene acts as the receptor for 2 cognate ligands, namely colony stimulating factor-1 (CSF-1) and interleukin-34 (IL-34). Here, we show that depletion in CSF-1R signalling induces BBB disruption and decreases the phagocytic capacity of peripheral macrophages but not microglia. CSF-1R signalling appears to be critical for macrophage and microglial activation, and macrophage localisation to amyloid appears reduced following the induction of Csf-1r heterozygosity in macrophages. Finally, we show that endothelial/microglial crosstalk and concomitant attenuation of CSF-1R signalling causes re-modelling of BBB-associated tight junctions and suggest that regulating BBB integrity and systemic macrophage recruitment to the brain may be therapeutically relevant in ALSP and other Alzheimer's-like dementias., (© 2020 The Authors. Published under the terms of the CC BY 4.0 license.)
- Published
- 2021
- Full Text
- View/download PDF
37. Natural Antibodies: Protecting Role of IgM in Glioblastoma and Brain Tumours.
- Author
-
Semwal S, Boukherroub R, Savvides SN, and Bouckaert J
- Subjects
- Humans, Immunoglobulin M, Tumor Microenvironment, Brain Neoplasms pathology, Glioblastoma drug therapy, Glioblastoma pathology
- 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 is available. Therefore, there is a need to search for 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 were 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, and WHO Globocan., Results and Conclusion: Currently, only a limited number of therapies are approved for GBM, and no standard care is in place in case of disease relapse, necessitating a possible broader perspective in looking at the disease and its underlying mechanisms., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)
- Published
- 2021
- Full Text
- View/download PDF
38. Rational Design and Development of HDAC Inhibitors for Breast Cancer Treatment.
- Author
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Mody D, Bouckaert J, Savvides SN, and Gupta V
- Subjects
- Female, Histone Deacetylases metabolism, Humans, Protein Isoforms, Histone Deacetylase Inhibitors chemistry, Histone Deacetylase Inhibitors pharmacology, Histone Deacetylase Inhibitors therapeutic use, Triple Negative Breast Neoplasms
- Abstract
Background: Breast cancer is the most prevalent cancer amongst females across the globe, and with over 2 million new cases reported in 2018, it poses a huge economic burden to the already dwindling public health. A dearth of therapies in the pipeline to treat triple-negative breast cancers and acquisition of resistance against the existing line of treatments urge the need to strategize novel therapeutics in order to add new drugs to the pipeline. HDAC inhibitors (HDACi) is one such class of small molecule inhibitors that target histone deacetylases to bring about chromosomal remodelling and normalize dysregulated gene expression that marks breast cancer progression., Objective: While four HDACi have been approved by the FDA for the treatment of different cancer types, no HDACi is specifically earmarked for clinical management of breast cancer. Owing to the differential HDAC expression pertaining to different types of breast cancers, isoform-selective HDAC inhibitors need to be discovered., Conclusion: This review attempts to set the stage for the rational structure-based discovery of isoform-selective HDACi by providing structural insights into different HDACs and their catalytic folds based on their classes and individual landscape. The development of inhibitors in accordance with the differential expression of HDAC isoforms exhibited in breast cancer cells is a promising strategy to rationally design selective and effective inhibitors, adopting a 'personalized-medicine' approach., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)
- Published
- 2021
- Full Text
- View/download PDF
39. Homogeneously N-glycosylated proteins derived from the GlycoDelete HEK293 cell line enable diffraction-quality crystallogenesis.
- Author
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Kozak S, Bloch Y, De Munck S, Mikula A, Bento I, Savvides SN, and Meijers R
- Subjects
- Cryoelectron Microscopy methods, Crystallography, X-Ray methods, Glycosylation, HEK293 Cells, Humans, Protein Processing, Post-Translational, Glycoproteins chemistry, Polysaccharides chemistry
- Abstract
Structural studies of glycoproteins and their complexes provide critical insights into their roles in normal physiology and disease. Most glycoproteins contain N-linked glycosylation, a key post-translation modification that critically affects protein folding and stability and the binding kinetics underlying protein interactions. However, N-linked glycosylation is often an impediment to yielding homogeneous protein preparations for structure determination by X-ray crystallography or other methods. In particular, obtaining diffraction-quality crystals of such proteins and their complexes often requires modification of both the type of glycosylation patterns and their extent. Here, we demonstrate the benefits of producing target glycoproteins in the GlycoDelete human embryonic kidney 293 cell line that has been engineered to produce N-glycans as short glycan stumps comprising N-acetylglucosamine, galactose and sialic acid. Protein fragments of human Down syndrome cell-adhesion molecule and colony-stimulating factor 1 receptor were obtained from the GlycoDelete cell line for crystallization. The ensuing reduction in the extent and complexity of N-glycosylation in both protein molecules compared with alternative glycoengineering approaches enabled their productive deployment in structural studies by X-ray crystallography. Furthermore, a third successful implementation of the GlycoDelete technology focusing on murine IL-12B is shown to lead to N-glycosylation featuring an immature glycan in diffraction-quality crystals. It is proposed that the GlycoDelete cell line could serve as a valuable go-to option for the production of homogeneous glycoproteins and their complexes for structural studies by X-ray crystallography and cryo-electron microscopy., (open access.)
- Published
- 2020
- Full Text
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40. Endeavors towards transformation of M. tuberculosis thymidylate kinase (MtbTMPK) inhibitors into potential antimycobacterial agents.
- Author
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Jian Y, Merceron R, De Munck S, Forbes HE, Hulpia F, Risseeuw MDP, Van Hecke K, Savvides SN, Munier-Lehmann H, Boshoff HIM, and Van Calenbergh S
- Subjects
- Antitubercular Agents chemistry, Antitubercular Agents pharmacology, Cell Line, Humans, Microbial Sensitivity Tests, Structure-Activity Relationship, Drug Design, Enzyme Inhibitors chemistry, Enzyme Inhibitors pharmacology, Mycobacterium tuberculosis drug effects, Mycobacterium tuberculosis enzymology, Nucleoside-Phosphate Kinase antagonists & inhibitors
- Abstract
As the last enzyme in nucleotide synthesis as precursors for DNA replication, thymidylate kinase of M. tuberculosis (MtbTMPK) attracts significant interest as a target in the discovery of new anti-tuberculosis agents. Earlier, we discovered potent MtbTMPK inhibitors, but these generally suffered from poor antimycobacterial activity, which we hypothesize is due to poor bacterial uptake. To address this, we herein describe our efforts to equip previously reported MtbTMPK inhibitors with targeting moieties to increase the whole cell activity of the hybrid analogues. Introduction of a simplified Fe-chelating siderophore motif gave rise to analogue 17 that combined favorable enzyme inhibitory activity with significant activity against M. tuberculosis (MIC of 12.5 μM). Conjugation of MtbTMPK inhibitors with an imidazo[1,2-a]pyridine or 3,5-dinitrobenzamide scaffold afforded analogues 26, 27 and 28, with moderate MtbTMPK enzyme inhibitory potency, but sub-micromolar activity against mycobacteria without significant cytotoxicity. These results indicate that conjugation with structural motifs known to favor mycobacterial uptake may be a valid approach for discovering new antimycobacterial agents., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Masson SAS. All rights reserved.)
- Published
- 2020
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41. An Avatar-Led Intervention Promotes Smoking Cessation in Young Adults: A Pilot Randomized Clinical Trial.
- Author
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Karekla M, Savvides SN, and Gloster A
- Subjects
- Cyprus, Female, Humans, Intention, Male, Motivation, Pilot Projects, Self Efficacy, Students psychology, Tobacco Use Disorder therapy, Universities, Young Adult, Acceptance and Commitment Therapy methods, Internet-Based Intervention, Smoking Cessation methods
- Abstract
Background: Smoking remains a global concern, especially for young adults. There is a dearth of smoking cessation programs for this population, who seldom seek help or are motivated to quit., Purpose: This pilot study assessed the effectiveness of a digital avatar-led Acceptance and Commitment Therapy (ACT) smoking cessation program (Flexiquit) for young adult smokers at all levels of motivation to quit., Methods: Smokers with no particular interest in quitting smoking (65.45% reported being in pre-contemplation or contemplation stages of change) were recruited from three universities (105 smoking ≥ 1 cigarette per day during the past 30 days, 68 females). Those who completed questionnaires online (N = 84; M = 22.44 years, SD = 2.61, range 18-28 years old) were randomized to either a six-session avatar-led intervention (Flexiquit; N = 49) or a wait-list control (N = 35). Primary outcomes included cessation status (7-day point prevalence) and number of cigarettes smoked per day; secondary outcomes were nicotine dependence, intention-to-quit smoking and self-efficacy, assessed at pre- and post-intervention, and only for Flexiquit at 6-month follow-up., Results: In intention-to-treat analysis more participants (OR = 3.10, 95% CI = 0.92-10.41) in the treatment group (28.57%) versus the control group (11.43%) reported quitting smoking; however, the difference was not statistically significant (p = .067). There were statistically significant decreases in average number of cigarettes, nicotine dependence and increases in self-efficacy, and intention-to-quit smoking compared to controls. Treatment gains in the Flexiquit group were maintained through the 6-month follow-up., Conclusions: An avatar-led digitized smoking cessation intervention based on ACT could increase the odds of quitting smoking. Findings suggest that a digitized program designed to engage young adults in smoking cessation may result in quitting smoking and has a high applicability potential especially among the hard-to-reach population of young adults., Question: Can an avatar-led digitized Acceptance and Commitment Therapy (ACT) smoking cessation intervention result in quitting smoking and increasing intention to quit among young smokers at various levels of motivation to quit, compared to a wait-list control group?, Findings: In this pilot randomized clinical trial that included 84 smokers, 28.57% in the treatment condition versus 11.43% in the wait-list control group were abstinent at post (intention-to-treat [ITT] analysis). An avatar-led digitized ACT smoking cessation intervention results in high quitting smoking rates and has a high applicability potential especially among the hard-to-reach population of young adult smokers., (© Society of Behavioral Medicine 2020. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
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- 2020
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42. Mouse Strain-Dependent Difference Toward the Staphylococcus aureus Allergen Serine Protease-Like Protein D Reveals a Novel Regulator of IL-33.
- Author
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Teufelberger AR, Van Nevel S, Hulpiau P, Nordengrün M, Savvides SN, De Graeve S, Akula S, Holtappels G, De Ruyck N, Declercq W, Vandenabeele P, Hellman L, Bröker BM, Krysko DV, Bachert C, and Krysko O
- Subjects
- Animals, Asthma immunology, Female, Frameshift Mutation immunology, Mice, Mice, Inbred BALB C, Mice, Inbred C57BL, Mice, Inbred CBA, Mice, Inbred DBA, Peptide Hydrolases immunology, Serine Endopeptidases immunology, Serpins immunology, Allergens immunology, Bacterial Proteins immunology, Interleukin-33 immunology, Serine Proteases immunology, Staphylococcal Infections immunology, Staphylococcus aureus immunology
- Abstract
Staphylococcus aureus ( S. aureus) can secrete a broad range of virulence factors, among which staphylococcal serine protease-like proteins (Spls) have been identified as bacterial allergens. The S. aureus allergen serine protease-like protein D (SplD) induces allergic asthma in C57BL/6J mice through the IL-33/ST2 signaling axis. Analysis of C57BL/6J, C57BL/6N, CBA, DBA/2, and BALB/c mice treated with intratracheal applications of SplD allowed us to identify a frameshift mutation in the serine (or cysteine) peptidase inhibitor, clade A, and member 3I (S erpina3i ) causing a truncated form of SERPINA3I in BALB/c, CBA, and DBA/2 mice. IL-33 is a key mediator of SplD-induced immunity and can be processed by proteases leading to its activation or degradation. Full-length SERPINA3I inhibits IL-33 degradation in vivo in the lungs of SplD-treated BALB/c mice and in vitro by direct inhibition of mMCP-4. Collectively, our results establish SERPINA3I as a regulator of IL-33 in the lungs following exposure to the bacterial allergen SplD, and that the asthma phenotypes of mouse strains may be strongly influenced by the observed frameshift mutation in S erpina3i . The analysis of this protease-serpin interaction network might help to identify predictive biomarkers for type-2 biased airway disease in individuals colonized by S. aureus ., (Copyright © 2020 Teufelberger, Van Nevel, Hulpiau, Nordengrün, Savvides, De Graeve, Akula, Holtappels, De Ruyck, Declercq, Vandenabeele, Hellman, Bröker, Krysko, Bachert and Krysko.)
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- 2020
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43. DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumor immunotolerance.
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D'Anna F, Van Dyck L, Xiong J, Zhao H, Berrens RV, Qian J, Bieniasz-Krzywiec P, Chandra V, Schoonjans L, Matthews J, De Smedt J, Minnoye L, Amorim R, Khorasanizadeh S, Yu Q, Zhao L, De Borre M, Savvides SN, Simon MC, Carmeliet P, Reik W, Rastinejad F, Mazzone M, Thienpont B, and Lambrechts D
- Subjects
- A549 Cells, Humans, Immune Tolerance, MCF-7 Cells, Basic Helix-Loop-Helix Transcription Factors metabolism, DNA Methylation, Hypoxia metabolism, Hypoxia-Inducible Factor 1 metabolism, Tumor Escape
- Abstract
Background: Hypoxia is pervasive in cancer and other diseases. Cells sense and adapt to hypoxia by activating hypoxia-inducible transcription factors (HIFs), but it is still an outstanding question why cell types differ in their transcriptional response to hypoxia., Results: We report that HIFs fail to bind CpG dinucleotides that are methylated in their consensus binding sequence, both in in vitro biochemical binding assays and in vivo studies of differentially methylated isogenic cell lines. Based on in silico structural modeling, we show that 5-methylcytosine indeed causes steric hindrance in the HIF binding pocket. A model wherein cell-type-specific methylation landscapes, as laid down by the differential expression and binding of other transcription factors under normoxia, control cell-type-specific hypoxia responses is observed. We also discover ectopic HIF binding sites in repeat regions which are normally methylated. Genetic and pharmacological DNA demethylation, but also cancer-associated DNA hypomethylation, expose these binding sites, inducing HIF-dependent expression of cryptic transcripts. In line with such cryptic transcripts being more prone to cause double-stranded RNA and viral mimicry, we observe low DNA methylation and high cryptic transcript expression in tumors with high immune checkpoint expression, but not in tumors with low immune checkpoint expression, where they would compromise tumor immunotolerance. In a low-immunogenic tumor model, DNA demethylation upregulates cryptic transcript expression in a HIF-dependent manner, causing immune activation and reducing tumor growth., Conclusions: Our data elucidate the mechanism underlying cell-type-specific responses to hypoxia and suggest DNA methylation and hypoxia to underlie tumor immunotolerance.
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- 2020
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44. Modulation of Signaling Mediated by TSLP and IL-7 in Inflammation, Autoimmune Diseases, and Cancer.
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Marković I and Savvides SN
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- Animals, Autoimmune Diseases etiology, Cytokines chemistry, Cytokines genetics, Disease Susceptibility, Genetic Variation, Humans, Inflammation etiology, Interleukin-7 chemistry, Interleukin-7 genetics, Neoplasms etiology, Receptors, Cytokine chemistry, Receptors, Cytokine metabolism, Receptors, Interleukin-7 chemistry, Receptors, Interleukin-7 metabolism, Structure-Activity Relationship, Autoimmune Diseases metabolism, Cytokines metabolism, Inflammation metabolism, Interleukin-7 metabolism, Neoplasms metabolism, Signal Transduction
- Abstract
Thymic Stromal Lymphopoietin (TSLP) and Interleukin-7 (IL-7) are widely studied cytokines within distinct branches of immunology. On one hand, TSLP is crucially important for mediating type 2 immunity at barrier surfaces and has been linked to widespread allergic and inflammatory diseases of the airways, skin, and gut. On the other hand, IL-7 operates at the foundations of T-cell and innate lymphoid cell (ILC) development and homeostasis and has been associated with cancer. Yet, TSLP and IL-7 are united by key commonalities in their structure and the structural basis of the receptor assemblies they mediate to initiate cellular signaling, in particular their cross-utilization of IL-7Rα. As therapeutic targeting of TSLP and IL-7 via diverse approaches is reaching advanced stages and in light of the plethora of mechanistic and structural data on receptor signaling mediated by the two cytokines, the time is ripe to provide integrated views of such knowledge. Here, we first discuss the major pathophysiological roles of TSLP and IL-7 in autoimmune diseases, inflammation and cancer. Subsequently, we curate structural and mechanistic knowledge about receptor assemblies mediated by the two cytokines. Finally, we review therapeutic avenues targeting TSLP and IL-7 signaling. We envision that such integrated view of the mechanism, structure, and modulation of signaling assemblies mediated by TSLP and IL-7 will enhance and fine-tune the development of more effective and selective approaches to further interrogate the role of TSLP and IL-7 in physiology and disease., (Copyright © 2020 Marković and Savvides.)
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- 2020
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45. Single-Chain Soluble Receptor Fusion Proteins as Versatile Cytokine Inhibitors.
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Holgado A, Braun H, Verstraete K, Vanneste D, Callewaert N, Savvides SN, Afonina IS, and Beyaert R
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- HEK293 Cells, Humans, Interleukin-13 antagonists & inhibitors, Interleukin-4 antagonists & inhibitors, Anti-Inflammatory Agents, Interleukin-33 antagonists & inhibitors, Recombinant Fusion Proteins
- Abstract
Cytokines are small secreted proteins that among many functions also play key roles in the orchestration of inflammation in host defense and disease. Over the past years, a large number of biologics have been developed to target cytokines in disease, amongst which soluble receptor fusion proteins have shown some promise in pre-clinical studies. We have previously shown proof-of-concept for the therapeutic targeting of interleukin (IL)-33 in airway inflammation using a newly developed biologic, termed IL-33trap, comprising the ectodomains of the cognate receptor ST2 and the co-receptor IL-1RAcP fused into a single-chain recombinant fusion protein. Here we extend the biophysical and biological characterization of IL-33trap variants, and show that IL-33trap is a stable protein with a monomeric profile both at physiological temperatures and during liquid storage at 4°C. Reducing the N-glycan heterogeneity and complexity of IL-33trap via GlycoDelete engineering neither affects its stability nor its inhibitory activity against IL-33. We also report that IL-33trap specifically targets biologically active IL-33 splice variants. Finally, we document the generation and antagonistic activity of a single-chain IL-4/13trap, which inhibits both IL-4 and IL-13 signaling. Collectively, these results illustrate that single-chain soluble receptor fusion proteins against IL-4, IL-13, and IL-33 are novel biologics that might not only be of interest for research purposes and further interrogation of the role of their target cytokines in physiology and disease, but may also complement monoclonal antibodies for the treatment of allergic and other inflammatory diseases., (Copyright © 2020 Holgado, Braun, Verstraete, Vanneste, Callewaert, Savvides, Afonina and Beyaert.)
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- 2020
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46. Structure and Assembly Mechanism of the Signaling Complex Mediated by Human CSF-1.
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Felix J, De Munck S, Verstraete K, Meuris L, Callewaert N, Elegheert J, and Savvides SN
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- 2020
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47. Small-molecule inhibitors get pro-inflammatory TNF into shape.
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Savvides SN and Elewaut D
- Subjects
- Signal Transduction, Tumor Necrosis Factor-alpha
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- 2020
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48. Charcot-Leyden crystals promote neutrophilic inflammation in patients with nasal polyposis.
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Gevaert E, Delemarre T, De Volder J, Zhang N, Holtappels G, De Ruyck N, Persson E, Heyndrickx I, Verstraete K, Aegerter H, Nauwynck H, Savvides SN, Lambrecht BN, and Bachert C
- Subjects
- Extracellular Traps immunology, Female, Galectins immunology, Humans, Inflammasomes immunology, Inflammation, Interleukin-1beta immunology, Male, NLR Family, Pyrin Domain-Containing 3 Protein immunology, Nasal Polyps immunology, Nasal Polyps pathology, Neutrophils immunology, Neutrophils pathology
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- 2020
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49. Activating mutations in CSF1R and additional receptor tyrosine kinases in histiocytic neoplasms.
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Durham BH, Lopez Rodrigo E, Picarsic J, Abramson D, Rotemberg V, De Munck S, Pannecoucke E, Lu SX, Pastore A, Yoshimi A, Mandelker D, Ceyhan-Birsoy O, Ulaner GA, Walsh M, Yabe M, Petrova-Drus K, Arcila ME, Ladanyi M, Solit DB, Berger MF, Hyman DM, Lacouture ME, Erickson C, Saganty R, Ki M, Dunkel IJ, Santa-María López V, Mora J, Haroche J, Emile JF, Decaux O, Geissmann F, Savvides SN, Drilon A, Diamond EL, and Abdel-Wahab O
- Subjects
- Adolescent, Adult, Aminopyridines pharmacology, Benzothiazoles pharmacology, Child, Child, Preschool, Female, Genome, Human, Hematologic Neoplasms drug therapy, Hematologic Neoplasms genetics, Hematologic Neoplasms pathology, Histiocytosis drug therapy, Histiocytosis pathology, Humans, Infant, Male, Mutation, Picolinic Acids pharmacology, Protein Kinase Inhibitors pharmacology, Pyrazoles pharmacology, Pyridines pharmacology, Pyrroles pharmacology, Receptor Protein-Tyrosine Kinases genetics, Twins, Monozygotic, Exome Sequencing, Young Adult, Anaplastic Lymphoma Kinase genetics, Histiocytosis genetics, Proto-Oncogene Proteins c-ret genetics, Receptors, Granulocyte-Macrophage Colony-Stimulating Factor genetics
- Abstract
Histiocytoses are clonal hematopoietic disorders frequently driven by mutations mapping to the BRAF and MEK1 and MEK2 kinases. Currently, however, the developmental origins of histiocytoses in patients are not well understood, and clinically meaningful therapeutic targets outside of BRAF and MEK are undefined. In this study, we uncovered activating mutations in CSF1R and rearrangements in RET and ALK that conferred dramatic responses to selective inhibition of RET (selpercatinib) and crizotinib, respectively, in patients with histiocytosis.
- Published
- 2019
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50. Pathophysiology and inhibition of IL-23 signaling in psoriatic arthritis: A molecular insight.
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Nguyen CT, Bloch Y, Składanowska K, Savvides SN, and Adamopoulos IE
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- Antibodies, Monoclonal, Humanized pharmacology, Antibodies, Monoclonal, Humanized therapeutic use, Dermatologic Agents therapeutic use, Humans, Ustekinumab pharmacology, Ustekinumab therapeutic use, Arthritis, Psoriatic drug therapy, Arthritis, Psoriatic physiopathology, Dermatologic Agents pharmacology, Interleukin-23 antagonists & inhibitors, Signal Transduction drug effects
- Abstract
Psoriatic arthritis (PsA) is a chronic inflammatory arthritis of unknown etiology, and currently the cellular and molecular interactions that dictate its pathogenesis remain elusive. A role of the interleukin-23 (IL-23)/IL-23R (IL-23 receptor) interaction in the development of psoriasis and PsA is well established. As IL-23 regulates the differentiation and activation of innate and adaptive immunity, it pertains to a very complex pathophysiology involving a plethora of effectors and transducers. In this review, we will discuss recent advances on the cellular and molecular pathophysiological mechanisms that regulate the initiation and progression of PsA as well as new therapeutic approaches for IL-23/IL-23R targeted therapeutics., (Copyright © 2018 Elsevier Inc. All rights reserved.)
- Published
- 2019
- Full Text
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