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Winkelmann H, Richter CP, Eising J, Piehler J, Kurre R. Correlative single-molecule and structured illumination microscopy of fast dynamics at the plasma membrane. Nat Commun 2024; 15:5813. [PMID: 38987559 PMCID: PMC11236984 DOI: 10.1038/s41467-024-49876-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 06/21/2024] [Indexed: 07/12/2024] Open
Abstract
Total internal reflection fluorescence (TIRF) microscopy offers powerful means to uncover the functional organization of proteins in the plasma membrane with very high spatial and temporal resolution. Traditional TIRF illumination, however, shows a Gaussian intensity profile, which is typically deteriorated by overlaying interference fringes hampering precise quantification of intensities-an important requisite for quantitative analyses in single-molecule localization microscopy (SMLM). Here, we combine flat-field illumination by using a standard πShaper with multi-angular TIR illumination by incorporating a spatial light modulator compatible with fast super-resolution structured illumination microscopy (SIM). This distinct combination enables quantitative multi-color SMLM with a highly homogenous illumination. By using a dual camera setup with optimized image splitting optics, we achieve a versatile combination of SMLM and SIM with up to three channels. We deploy this setup for establishing robust detection of receptor stoichiometries based on single-molecule intensity analysis and single-molecule Förster resonance energy transfer (smFRET). Homogeneous illumination furthermore enables long-term tracking and localization microscopy (TALM) of cell surface receptors identifying spatial heterogeneity of mobility and accessibility in the plasma membrane. By combination of TALM and SIM, spatially and molecularly heterogenous diffusion properties can be correlated with nanoscale cytoskeletal organization and dynamics.
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Affiliation(s)
- Hauke Winkelmann
- Division of Biophysics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany
| | - Christian P Richter
- Division of Biophysics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany
| | - Jasper Eising
- Division of Biophysics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany
| | - Jacob Piehler
- Division of Biophysics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany.
- Center for Cellular Nanoanalytics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany.
| | - Rainer Kurre
- Division of Biophysics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany.
- Center for Cellular Nanoanalytics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany.
- Integrated Bioimaging Facility iBiOs, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany.
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2
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Sinha S, Hembram KC, Chatterjee S. Targeting signaling pathways in cancer stem cells: A potential approach for developing novel anti-cancer therapeutics. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 385:157-209. [PMID: 38663959 DOI: 10.1016/bs.ircmb.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Cancer stem cells (CSCs) have emerged as prime players in the intricate landscape of cancer development, progression, and resistance to traditional treatments. These unique cellular subpopulations own the remarkable capability of self-renewal and differentiation, giving rise to the diverse cellular makeup of tumors and fostering their recurrence following conventional therapies. In the quest for developing more effective cancer therapeutics, the focus has now shifted toward targeting the signaling pathways that govern CSCs behavior. This chapter underscores the significance of these signaling pathways in CSC biology and their potential as pivotal targets for the development of novel chemotherapy approaches. We delve into several key signaling pathways essential for maintaining the defining characteristics of CSCs, including the Wnt, Hedgehog, Notch, JAK-STAT, NF-κB pathways, among others, shedding light on their potential crosstalk. Furthermore, we highlight the latest advancements in CSC-targeted therapies, spanning from promising preclinical models to ongoing clinical trials. A comprehensive understanding of the intricate molecular aspects of CSC signaling pathways and their manipulation holds the prospective to revolutionize cancer treatment paradigms. This, in turn, could lead to more efficacious and personalized therapies with the ultimate goal of eradicating CSCs and enhancing overall patient outcomes. The exploration of CSC signaling pathways represents a key step towards a brighter future in the battle against cancer.
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Affiliation(s)
- Saptarshi Sinha
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | | | - Subhajit Chatterjee
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, United States.
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3
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Saiyed N, Yilmaz A, Vishweswariah S, Maiti AK, Ustun I, Bartolone S, Brown-Hughes T, Thorpe RJ, Osentoski T, Ruff S, Pai A, Maddens M, Imam K, Graham SF. Urinary Cytokines as Potential Biomarkers of Mild Cognitive Impairment and Alzheimer's Disease: A Pilot Study. J Alzheimers Dis Rep 2023; 7:649-657. [PMID: 37483327 PMCID: PMC10357120 DOI: 10.3233/adr-220081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 05/13/2023] [Indexed: 07/25/2023] Open
Abstract
Background Alzheimer's disease (AD) is the most common form of dementia, accounting for 80% of all cases. Mild cognitive impairment (MCI) is a transitional state between normal aging and AD. Early detection is crucial, as irreversible brain damage occurs before symptoms manifest. Objective This study aimed to identify potential biomarkers for early detection of AD by analyzing urinary cytokine concentrations. We investigated 37 cytokines in AD, MCI, and cognitively normal individuals (NC), assessing their associations with AD development. Methods Urinary cytokine concentrations were measured in AD (n = 25), MCI (n = 25), and NC (n = 26) patients. IL6ST and MMP-2 levels were compared between AD and NC, while TNFRSF8, IL6ST, and IL-19 were assessed in AD versus MCI. Diagnostic models distinguished AD from NC, and in-silico analysis explored molecular mechanisms related to AD. Results Significant perturbations in IL6ST and MMP-2 concentrations were observed in AD urine compared to NC, suggesting their potential as biomarkers. TNFRSF8, IL6ST, and IL-19 differed significantly between AD and MCI, implicating them in disease progression. Diagnostic models exhibited promising performance (AUC: 0.59-0.79, sensitivity: 0.72-0.80, specificity: 0.56-0.78) in distinguishing AD from NC. In-silico analysis revealed molecular insights, including relevant non-coding RNAs, microRNAs, and transcription factors. Conclusion This study establishes significant associations between urinary cytokine concentrations and AD and MCI. IL6ST, MMP-2, TNFRSF8, IL6ST, and IL-19 emerge as potential biomarkers for early detection of AD. In-silico analysis enhances understanding of molecular mechanisms in AD. Further validation and exploration of these biomarkers in larger cohorts are warranted to assess their clinical utility.
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Affiliation(s)
- Nazia Saiyed
- Beaumont Research Institute, Metabolomics Department, Royal Oak, MI, USA
| | - Ali Yilmaz
- Beaumont Research Institute, Metabolomics Department, Royal Oak, MI, USA
- Oakland University-William Beaumont School of Medicine, Rochester, MI, USA
| | | | - Amit K. Maiti
- Department of Genetics and Genomics, Mydnavar, Southfield, MI, USA
| | - Ilyas Ustun
- College of Computing and Digital Media, DePaul University, Chicago, IL, USA
| | - Sarah Bartolone
- Department of Urology, Beaumont Research Institute, Royal Oak, MI, USA
| | | | - Roland J. Thorpe
- Department of Health, Behavior, and Society, Program for Research on Men’s Health, Hopkins Center for Health Disparities Solutions, Johns Hopkins Alzheimer’s Disease Resource Center for Minority Aging Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Tammy Osentoski
- Department of Alzheimer’s Research, Beaumont Health, Royal Oak, MI, USA
| | - Stacey Ruff
- Beaumont Health, Geriatric Medicine, Berkley, MI, USA
| | - Amita Pai
- Beaumont Health, Geriatric Medicine, Berkley, MI, USA
| | | | - Khaled Imam
- Beaumont Health, Geriatric Medicine, Berkley, MI, USA
| | - Stewart F. Graham
- Beaumont Research Institute, Metabolomics Department, Royal Oak, MI, USA
- Oakland University-William Beaumont School of Medicine, Rochester, MI, USA
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4
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McFarlane A, Pohler E, Moraga I. Molecular and cellular factors determining the functional pleiotropy of cytokines. FEBS J 2023; 290:2525-2552. [PMID: 35246947 PMCID: PMC10952290 DOI: 10.1111/febs.16420] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/26/2022] [Accepted: 03/03/2022] [Indexed: 11/30/2022]
Abstract
Cytokines are soluble factors vital for mammalian physiology. Cytokines elicit highly pleiotropic activities, characterized by their ability to induce a wide spectrum of functional responses in a diverse range of cell subsets, which makes their study very challenging. Cytokines activate signalling via receptor dimerization/oligomerization, triggering activation of the JAK (Janus kinase)/STAT (signal transducer and activator of transcription) signalling pathway. Given the strong crosstalk and shared usage of key components of cytokine signalling pathways, a long-standing question in the field pertains to how functional diversity is achieved by cytokines. Here, we discuss how biophysical - for example, ligand-receptor binding affinity and topology - and cellular - for example, receptor, JAK and STAT protein levels, endosomal compartment - parameters contribute to the modulation and diversification of cytokine responses. We review how these parameters ultimately converge into a common mechanism to fine-tune cytokine signalling that involves the control of the number of Tyr residues phosphorylated in the receptor intracellular domain upon cytokine stimulation. This results in different kinetics of STAT activation, and induction of specific gene expression programs, ensuring the generation of functional diversity by cytokines using a limited set of signalling intermediaries. We describe how these first principles of cytokine signalling have been exploited using protein engineering to design cytokine variants with more specific and less toxic responses for immunotherapy.
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Affiliation(s)
- Alison McFarlane
- Division of Cell Signalling and ImmunologySchool of Life SciencesUniversity of DundeeUK
| | - Elizabeth Pohler
- Division of Cell Signalling and ImmunologySchool of Life SciencesUniversity of DundeeUK
| | - Ignacio Moraga
- Division of Cell Signalling and ImmunologySchool of Life SciencesUniversity of DundeeUK
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5
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Frenay J, Bellaye PS, Oudot A, Helbling A, Petitot C, Ferrand C, Collin B, Dias AMM. IL-1RAP, a Key Therapeutic Target in Cancer. Int J Mol Sci 2022; 23:ijms232314918. [PMID: 36499246 PMCID: PMC9735758 DOI: 10.3390/ijms232314918] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 11/30/2022] Open
Abstract
Cancer is a major cause of death worldwide and especially in high- and upper-middle-income countries. Despite recent progress in cancer therapies, such as chimeric antigen receptor T (CAR-T) cells or antibody-drug conjugate (ADC), new targets expressed by the tumor cells need to be identified in order to selectively drive these innovative therapies to tumors. In this context, IL-1RAP recently showed great potential to become one of these new targets for cancer therapy. IL-1RAP is highly involved in the inflammation process through the interleukins 1, 33, and 36 (IL-1, IL-33, IL-36) signaling pathways. Inflammation is now recognized as a hallmark of carcinogenesis, suggesting that IL-1RAP could play a role in cancer development and progression. Furthermore, IL-1RAP was found overexpressed on tumor cells from several hematological and solid cancers, thus confirming its potential involvement in carcinogenesis. This review will first describe the structure and genetics of IL-1RAP as well as its role in tumor development. Finally, a focus will be made on the therapies based on IL-1RAP targeting, which are now under preclinical or clinical development.
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Affiliation(s)
- Jame Frenay
- Plateforme d'Imagerie et Radiothérapie Précliniques, Médecine Nucléaire, Centre Georges-François Leclerc, 21000 Dijon, France
| | - Pierre-Simon Bellaye
- Plateforme d'Imagerie et Radiothérapie Précliniques, Médecine Nucléaire, Centre Georges-François Leclerc, 21000 Dijon, France
| | - Alexandra Oudot
- Plateforme d'Imagerie et Radiothérapie Précliniques, Médecine Nucléaire, Centre Georges-François Leclerc, 21000 Dijon, France
| | - Alex Helbling
- Plateforme d'Imagerie et Radiothérapie Précliniques, Médecine Nucléaire, Centre Georges-François Leclerc, 21000 Dijon, France
| | - Camille Petitot
- Plateforme d'Imagerie et Radiothérapie Précliniques, Médecine Nucléaire, Centre Georges-François Leclerc, 21000 Dijon, France
| | - Christophe Ferrand
- INSERM UMR1098, EFS BFC, Université de Bourgogne Franche-Comté, 25000 Besançon, France
- CanCell Therapeutics, 25000 Besançon, France
| | - Bertrand Collin
- Plateforme d'Imagerie et Radiothérapie Précliniques, Médecine Nucléaire, Centre Georges-François Leclerc, 21000 Dijon, France
- Institut de Chimie Moléculaire de l'Université de Bourgogne, UMR CNRS 6302, 21000 Dijon, France
| | - Alexandre M M Dias
- Plateforme d'Imagerie et Radiothérapie Précliniques, Médecine Nucléaire, Centre Georges-François Leclerc, 21000 Dijon, France
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6
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VanDyke D, Iglesias M, Tomala J, Young A, Smith J, Perry JA, Gebara E, Cross AR, Cheung LS, Dykema AG, Orcutt-Jahns BT, Henclová T, Golias J, Balolong J, Tomasovic LM, Funda D, Meyer AS, Pardoll DM, Hester J, Issa F, Hunter CA, Anderson MS, Bluestone JA, Raimondi G, Spangler JB. Engineered human cytokine/antibody fusion proteins expand regulatory T cells and confer autoimmune disease protection. Cell Rep 2022; 41:111478. [PMID: 36261022 PMCID: PMC9631798 DOI: 10.1016/j.celrep.2022.111478] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/02/2022] [Accepted: 09/20/2022] [Indexed: 11/12/2022] Open
Abstract
Low-dose human interleukin-2 (hIL-2) treatment is used clinically to treat autoimmune disorders due to the cytokine's preferential expansion of immunosuppressive regulatory T cells (Tregs). However, off-target immune cell activation and short serum half-life limit the clinical potential of IL-2 treatment. Recent work showed that complexes comprising hIL-2 and the anti-hIL-2 antibody F5111 overcome these limitations by preferentially stimulating Tregs over immune effector cells. Although promising, therapeutic translation of this approach is complicated by the need to optimize dosing ratios and by the instability of the cytokine/antibody complex. We leverage structural insights to engineer a single-chain hIL-2/F5111 antibody fusion protein, termed F5111 immunocytokine (IC), which potently and selectively activates and expands Tregs. F5111 IC confers protection in mouse models of colitis and checkpoint inhibitor-induced diabetes mellitus. These results provide a roadmap for IC design and establish a Treg-biased immunotherapy that could be clinically translated for autoimmune disease treatment.
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Affiliation(s)
- Derek VanDyke
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Marcos Iglesias
- Vascularized Composite Allotransplantation Laboratory, Department of Plastic and Reconstructive Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jakub Tomala
- Institute of Biotechnology of the Academy of Sciences of the Czech Republic, Vestec 252 50, Czech Republic
| | - Arabella Young
- Diabetes Center, University of California San Francisco, San Francisco, CA 94143, USA; Sean N. Parker Autoimmune Research Laboratory, University of California San Francisco, San Francisco, CA 94143, USA; Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA; Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Jennifer Smith
- Diabetes Center, University of California San Francisco, San Francisco, CA 94143, USA
| | - Joseph A Perry
- Department of Pathobiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Edward Gebara
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Amy R Cross
- Translational Research Immunology Group, Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK
| | - Laurene S Cheung
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21231, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Arbor G Dykema
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21231, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Brian T Orcutt-Jahns
- Department of Bioengineering, Jonsson Comprehensive Cancer Center, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tereza Henclová
- Institute of Biotechnology of the Academy of Sciences of the Czech Republic, Vestec 252 50, Czech Republic
| | - Jaroslav Golias
- Institute of Microbiology of the Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Jared Balolong
- Diabetes Center, University of California San Francisco, San Francisco, CA 94143, USA
| | - Luke M Tomasovic
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - David Funda
- Institute of Microbiology of the Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Aaron S Meyer
- Department of Bioengineering, Jonsson Comprehensive Cancer Center, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Drew M Pardoll
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21231, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Joanna Hester
- Translational Research Immunology Group, Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK
| | - Fadi Issa
- Translational Research Immunology Group, Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK
| | - Christopher A Hunter
- Department of Pathobiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mark S Anderson
- Diabetes Center, University of California San Francisco, San Francisco, CA 94143, USA
| | - Jeffrey A Bluestone
- Diabetes Center, University of California San Francisco, San Francisco, CA 94143, USA; Sean N. Parker Autoimmune Research Laboratory, University of California San Francisco, San Francisco, CA 94143, USA; Sonoma Biotherapeutics, South San Francisco, CA 94080, USA
| | - Giorgio Raimondi
- Vascularized Composite Allotransplantation Laboratory, Department of Plastic and Reconstructive Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jamie B Spangler
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21231, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21231, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
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7
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Schamber MR, Vafabakhsh R. Mechanism of sensitivity modulation in the calcium-sensing receptor via electrostatic tuning. Nat Commun 2022; 13:2194. [PMID: 35459864 PMCID: PMC9033857 DOI: 10.1038/s41467-022-29897-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 04/05/2022] [Indexed: 02/08/2023] Open
Abstract
Transfer of information across membranes is fundamental to the function of all organisms and is primarily initiated by transmembrane receptors. For many receptors, how ligand sensitivity is fine-tuned and how disease associated mutations modulate receptor conformation to allosterically affect receptor sensitivity are unknown. Here we map the activation of the calcium-sensing receptor (CaSR) - a dimeric class C G protein-coupled receptor (GPCR) and responsible for maintaining extracellular calcium in vertebrates. We show that CaSR undergoes unique conformational rearrangements compared to other class C GPCRs owing to specific structural features. Moreover, by analyzing disease associated mutations, we uncover a large permissiveness in the architecture of the extracellular domain of CaSR, with dynamics- and not specific receptor topology- determining the effect of a mutation. We show a structural hub at the dimer interface allosterically controls CaSR activation via focused electrostatic repulsion. Changes in the surface charge distribution of this hub, which is highly variable between organisms, finely tune CaSR sensitivity. This is potentially a general tuning mechanism for other dimeric receptors.
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Affiliation(s)
- Michael R Schamber
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.
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8
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Yen M, Ren J, Liu Q, Glassman CR, Sheahan TP, Picton LK, Moreira FR, Rustagi A, Jude KM, Zhao X, Blish CA, Baric RS, Su LL, Garcia KC. Facile discovery of surrogate cytokine agonists. Cell 2022; 185:1414-1430.e19. [PMID: 35325595 PMCID: PMC9021867 DOI: 10.1016/j.cell.2022.02.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/11/2022] [Accepted: 02/22/2022] [Indexed: 12/26/2022]
Abstract
Cytokines are powerful immune modulators that initiate signaling through receptor dimerization, but natural cytokines have structural limitations as therapeutics. We present a strategy to discover cytokine surrogate agonists by using modular ligands that exploit induced proximity and receptor dimer geometry as pharmacological metrics amenable to high-throughput screening. Using VHH and scFv to human interleukin-2/15, type-I interferon, and interleukin-10 receptors, we generated combinatorial matrices of single-chain bispecific ligands that exhibited diverse spectrums of functional activities, including potent inhibition of SARS-CoV-2 by surrogate interferons. Crystal structures of IL-2R:VHH complexes revealed that variation in receptor dimer geometries resulted in functionally diverse signaling outputs. This modular platform enabled engineering of surrogate ligands that compelled assembly of an IL-2R/IL-10R heterodimer, which does not naturally exist, that signaled through pSTAT5 on T and natural killer (NK) cells. This "cytokine med-chem" approach, rooted in principles of induced proximity, is generalizable for discovery of diversified agonists for many ligand-receptor systems.
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Affiliation(s)
- Michelle Yen
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Junming Ren
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Qingxiang Liu
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Caleb R Glassman
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Timothy P Sheahan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lora K Picton
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Fernando R Moreira
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Arjun Rustagi
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kevin M Jude
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xiang Zhao
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Catherine A Blish
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Ralph S Baric
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Leon L Su
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - K Christopher Garcia
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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9
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Glassman CR, Tsutsumi N, Saxton RA, Lupardus PJ, Jude KM, Garcia KC. Structure of a Janus kinase cytokine receptor complex reveals the basis for dimeric activation. Science 2022; 376:163-169. [PMID: 35271300 PMCID: PMC9306331 DOI: 10.1126/science.abn8933] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cytokines signal through cell surface receptor dimers to initiate activation of intracellular Janus Kinases (JAKs). We report the 3.6-Å resolution cryo-EM structure of full-length JAK1 complexed with a cytokine receptor intracellular Box1/Box2 domain, captured as an activated homodimer bearing the Val→Phe (VF) mutation prevalent in myeloproliferative neoplasms. The seven domains of JAK1 form an extended structural unit whose dimerization is mediated by close-packed pseudokinase (PK) domains. The oncogenic VF mutation lies within the core of the JAK1 PK dimer interface, enhancing packing complementarity to facilitate ligand-independent activation. The C-terminal tyrosine kinase domains are poised to phosphorylate the receptor STAT-recruiting motifs projecting from the overhanging FERM-SH2 domains. Mapping of constitutively active JAK mutants supports a two-step allosteric activation mechanism and reveals new opportunities for selective therapeutic targeting of oncogenic JAK signaling.
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Affiliation(s)
- Caleb R Glassman
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Naotaka Tsutsumi
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Robert A Saxton
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Patrick J Lupardus
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kevin M Jude
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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10
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Sotolongo Bellón J, Birkholz O, Richter CP, Eull F, Kenneweg H, Wilmes S, Rothbauer U, You C, Walter MR, Kurre R, Piehler J. Four-color single-molecule imaging with engineered tags resolves the molecular architecture of signaling complexes in the plasma membrane. CELL REPORTS METHODS 2022; 2:100165. [PMID: 35474965 PMCID: PMC9017138 DOI: 10.1016/j.crmeth.2022.100165] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/19/2021] [Accepted: 01/13/2022] [Indexed: 12/22/2022]
Abstract
Localization and tracking of individual receptors by single-molecule imaging opens unique possibilities to unravel the assembly and dynamics of signaling complexes in the plasma membrane. We present a comprehensive workflow for imaging and analyzing receptor diffusion and interaction in live cells at single molecule level with up to four colors. Two engineered, monomeric GFP variants, which are orthogonally recognized by anti-GFP nanobodies, are employed for efficient and selective labeling of target proteins in the plasma membrane with photostable fluorescence dyes. This labeling technique enables us to quantitatively resolve the stoichiometry and dynamics of the interferon-γ (IFNγ) receptor signaling complex in the plasma membrane of living cells by multicolor single-molecule imaging. Based on versatile spatial and spatiotemporal correlation analyses, we identify ligand-induced receptor homo- and heterodimerization. Multicolor single-molecule co-tracking and quantitative single-molecule Förster resonance energy transfer moreover reveals transient assembly of IFNγ receptor heterotetramers and confirms its structural architecture.
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Affiliation(s)
- Junel Sotolongo Bellón
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Oliver Birkholz
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Christian P. Richter
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Florian Eull
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Hella Kenneweg
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Stephan Wilmes
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
- Division of Cell Signalling and Immunology, University of Dundee, School of Life Sciences, Dundee, UK
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard-Karls-University, Tübingen, Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Changjiang You
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Mark R. Walter
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rainer Kurre
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Jacob Piehler
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
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11
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Drees C, Rühl P, Czerny J, Chandra G, Bajorath J, Haase M, Heinemann SH, Piehler J. Diffraction-Unlimited Photomanipulation at the Plasma Membrane via Specifically Targeted Upconversion Nanoparticles. NANO LETTERS 2021; 21:8025-8034. [PMID: 34519216 DOI: 10.1021/acs.nanolett.1c02267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Engineered UCNP are used to trigger rapid photoconversion of the fluorescent protein Dendra2 with nanoscopic precision and over longer distances in mammalian cells. By exploiting the synergy of high-level thulium doping with core-shell design and elevated excitation intensities, intense UCNP emission is achieved, allowing fast photoconversion of Dendra2 with <10 nm resolution. A tailored biocompatible surface coating and functionalization with a derivate of green fluorescent protein (GFP) for recognition of antiGFP nanobodies are developed. Highly specific targeting of UCNP to fusion proteins of antiGFP on the surface of mammalian cells is demonstrated. UCNP bound to extracellular Dendra2 enable rapid photoconversion selectively in molecular proximity and thus unambiguous detection of cytokine receptor dimerization in the plasma membrane and in endosomes. Remarkably, UCNPs are also suited for manipulating intracellular Dendra2 across the plasma membrane. This study thus establishes UCNP-controlled photomanipulation with nanoscale precision, opening exciting opportunities for bioanalytical applications in cell biology.
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Affiliation(s)
- Christoph Drees
- Department of Biology/Chemistry and Center of Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076 Osnabrück, Germany
| | - Philipp Rühl
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, 07745 Jena, Germany
| | - Jacqueline Czerny
- Department of Biology/Chemistry and Center of Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076 Osnabrück, Germany
| | - Gemini Chandra
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, 07745 Jena, Germany
| | - Janosch Bajorath
- Department of Biology/Chemistry and Center of Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076 Osnabrück, Germany
| | - Markus Haase
- Department of Biology/Chemistry and Center of Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076 Osnabrück, Germany
| | - Stefan H Heinemann
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, 07745 Jena, Germany
| | - Jacob Piehler
- Department of Biology/Chemistry and Center of Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076 Osnabrück, Germany
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12
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Functional Consequences of Mutations in Myeloproliferative Neoplasms. Hemasphere 2021; 5:e578. [PMID: 34095761 PMCID: PMC8171364 DOI: 10.1097/hs9.0000000000000578] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 04/13/2021] [Indexed: 01/14/2023] Open
Abstract
Driver mutations occur in Janus kinase 2 (JAK2), thrombopoietin receptor (MPL), and calreticulin (CALR) in BCR-ABL1 negative myeloproliferative neoplasms (MPNs). From mutations leading to one amino acid substitution in JAK2 or MPL, to frameshift mutations in CALR resulting in a protein with a different C-terminus, all the mutated proteins lead to pathologic and persistent JAK2-STAT5 activation. The most prevalent mutation, JAK2 V617F, is associated with the 3 entities polycythemia vera (PV), essential thrombocythemia (ET), and myelofibrosis (MF), while CALR and MPL mutations are associated only with ET and MF. Triple negative ET and MF patients may harbor noncanonical mutations in JAK2 or MPL. One major fundamental question is whether the conformations of JAK2 V617F, MPL W515K/L/A, or CALR mutants differ from those of their wild type counterparts so that a specific treatment could target the clone carrying the mutated driver and spare physiological hematopoiesis. Of great interest, a set of epigenetic mutations can co-exist with the phenotypic driver mutations in 35%–40% of MPNs. These epigenetic mutations, such as TET2, EZH2, ASXL1, or DNMT3A mutations, promote clonal hematopoiesis and increased fitness of aged hematopoietic stem cells in both clonal hematopoiesis of indeterminate potential (CHIP) and MPNs. Importantly, the main MPN driver mutation JAK2 V617F is also associated with CHIP. Accumulation of several epigenetic and splicing mutations favors progression of MPNs to secondary acute myeloid leukemia. Another major fundamental question is how epigenetic rewiring due to these mutations interacts with persistent JAK2-STAT5 signaling. Answers to these questions are required for better therapeutic interventions aimed at preventing progression of ET and PV to MF, and transformation of these MPNs in secondary acute myeloid leukemia.
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Prado J, Westerink RHS, Popov-Celeketic J, Steen-Louws C, Pandit A, Versteeg S, van de Worp W, Kanters DHAJ, Reedquist KA, Koenderman L, Hack CE, Eijkelkamp N. Cytokine receptor clustering in sensory neurons with an engineered cytokine fusion protein triggers unique pain resolution pathways. Proc Natl Acad Sci U S A 2021; 118:e2009647118. [PMID: 33836560 PMCID: PMC7980471 DOI: 10.1073/pnas.2009647118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
New therapeutic approaches to resolve persistent pain are highly needed. We tested the hypothesis that manipulation of cytokine receptors on sensory neurons by clustering regulatory cytokine receptor pairs with a fusion protein of interleukin (IL)-4 and IL-10 (IL4-10 FP) would redirect signaling pathways to optimally boost pain-resolution pathways. We demonstrate that a population of mouse sensory neurons express both receptors for the regulatory cytokines IL-4 and IL-10. This population increases during persistent inflammatory pain. Triggering these receptors with IL4-10 FP has unheralded biological effects, because it resolves inflammatory pain in both male and female mice. Knockdown of both IL4 and IL10 receptors in sensory neurons in vivo ablated the IL4-10 FP-mediated inhibition of inflammatory pain. Knockdown of either one of the receptors prevented the analgesic gain-of-function of IL4-10 FP. In vitro, IL4-10 FP inhibited inflammatory mediator-induced neuronal sensitization more effectively than the combination of cytokines, confirming its superior activity. The IL4-10 FP, contrary to the combination of IL-4 and IL-10, promoted clustering of IL-4 and IL-10 receptors in sensory neurons, leading to unique signaling, that is exemplified by activation of shifts in the cellular kinome and transcriptome. Interrogation of the potentially involved signal pathways led us to identify JAK1 as a key downstream signaling element that mediates the superior analgesic effects of IL4-10 FP. Thus, IL4-10 FP constitutes an immune-biologic that clusters regulatory cytokine receptors in sensory neurons to transduce unique signaling pathways required for full resolution of persistent inflammatory pain.
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Affiliation(s)
- Judith Prado
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, The Netherlands
| | - Remco H S Westerink
- Neurotoxicology Research Group, Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands
| | - Jelena Popov-Celeketic
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, The Netherlands
| | - Cristine Steen-Louws
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, The Netherlands
| | - Aridaman Pandit
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, The Netherlands
| | - Sabine Versteeg
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, The Netherlands
| | - Wouter van de Worp
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, The Netherlands
| | - Deon H A J Kanters
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, The Netherlands
| | - Kris A Reedquist
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, The Netherlands
| | - Leo Koenderman
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, The Netherlands
| | - C Erik Hack
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, The Netherlands
| | - Niels Eijkelkamp
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, The Netherlands;
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14
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Shi J, Song X, Traub B, Luxenhofer M, Kornmann M. Involvement of IL-4, IL-13 and Their Receptors in Pancreatic Cancer. Int J Mol Sci 2021; 22:ijms22062998. [PMID: 33804263 PMCID: PMC8000536 DOI: 10.3390/ijms22062998] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 01/05/2023] Open
Abstract
Interleukin (IL)-4 and IL-13 are known as pleiotropic Th2 cytokines with a wide range of biological properties and functions especially in immune responses. In addition, increasing activities have also been determined in oncogenesis and tumor progression of several malignancies. It is now generally accepted that IL-4 and IL-13 can exert effects on epithelial tumor cells through corresponding receptors. Type II IL-4 receptor (IL-4Rα/IL-13Rα1), predominantly expressed in non-hematopoietic cells, is identified to be the main target for both IL-4 and IL-13 in tumors. Moreover, IL-13 can also signal by binding to the IL-13Rα2 receptor. Structural similarity due to the use of the same receptor complex generated in response to IL-4/IL-13 results in overlapping but also distinct signaling pathways and functions. The aim of this review was to summarize knowledge about IL-4 and IL-13 and their receptors in pancreatic cancer in order understand the implication of IL-4 and IL-13 and their receptors for pancreatic tumorigenesis and progression and for developing possible new diagnostic and therapeutic targets.
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15
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Martinez-Fabregas J, Wang L, Pohler E, Cozzani A, Wilmes S, Kazemian M, Mitra S, Moraga I. CDK8 Fine-Tunes IL-6 Transcriptional Activities by Limiting STAT3 Resident Time at the Gene Loci. Cell Rep 2020; 33:108545. [PMID: 33357429 PMCID: PMC7773550 DOI: 10.1016/j.celrep.2020.108545] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/28/2020] [Accepted: 11/30/2020] [Indexed: 02/07/2023] Open
Abstract
Cytokines are highly pleiotropic ligands that regulate the immune response. Here, using interleukin-6 (IL-6) as a model system, we perform detailed phosphoproteomic and transcriptomic studies in human CD4+ T helper 1 (Th-1) cells to address the molecular bases defining cytokine functional pleiotropy. We identify CDK8 as a negative regulator of STAT3 transcriptional activities, which interacts with STAT3 upon IL-6 stimulation. Inhibition of CDK8 activity, using specific small molecule inhibitors, reduces the IL-6-induced phosphoproteome by 23% in Th-1 cells, including STAT3 S727 phosphorylation. STAT3 binding to target DNA sites in the genome is increased upon CDK8 inhibition, which results in a concomitant increase in STAT3-mediated transcriptional activity. Importantly, inhibition of CDK8 activity under Th-17 polarizing conditions results in an enhancement of Th-17 differentiation. Our results support a model where CDK8 regulates STAT3 transcriptional processivity by modulation of its gene loci resident time, critically contributing to diversification of IL-6 responses. CDK8 regulates IL-6-mediated STAT3 S727 phosphorylation in primary human T cells CDK8 controls STAT3 activity by limiting its resident time at gene loci CDK8 inhibition increases IL-6-mediated Th17 differentiation
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Affiliation(s)
| | - Luopin Wang
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Elizabeth Pohler
- Division of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Adeline Cozzani
- Université de Lille, INSERM UMR1277 CNRS UMR9020-CANTHER and Institut pour la Recherche sur le Cancer de Lille (IRCL), Lille, France
| | - Stephan Wilmes
- Division of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Majid Kazemian
- Department of Computer Science, Purdue University, West Lafayette, IN, USA; Department of Biochemistry, Purdue University, West Lafayette, IN, USA.
| | - Suman Mitra
- Université de Lille, INSERM UMR1277 CNRS UMR9020-CANTHER and Institut pour la Recherche sur le Cancer de Lille (IRCL), Lille, France.
| | - Ignacio Moraga
- Division of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK.
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17
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Wilmes S, Hafer M, Vuorio J, Tucker JA, Winkelmann H, Löchte S, Stanly TA, Pulgar Prieto KD, Poojari C, Sharma V, Richter CP, Kurre R, Hubbard SR, Garcia KC, Moraga I, Vattulainen I, Hitchcock IS, Piehler J. Mechanism of homodimeric cytokine receptor activation and dysregulation by oncogenic mutations. Science 2020; 367:643-652. [PMID: 32029621 PMCID: PMC8117407 DOI: 10.1126/science.aaw3242] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 10/08/2019] [Accepted: 12/20/2019] [Indexed: 12/11/2022]
Abstract
Homodimeric class I cytokine receptors are assumed to exist as preformed dimers that are activated by ligand-induced conformational changes. We quantified the dimerization of three prototypic class I cytokine receptors in the plasma membrane of living cells by single-molecule fluorescence microscopy. Spatial and spatiotemporal correlation of individual receptor subunits showed ligand-induced dimerization and revealed that the associated Janus kinase 2 (JAK2) dimerizes through its pseudokinase domain. Oncogenic receptor and hyperactive JAK2 mutants promoted ligand-independent dimerization, highlighting the formation of receptor dimers as the switch responsible for signal activation. Atomistic modeling and molecular dynamics simulations based on a detailed energetic analysis of the interactions involved in dimerization yielded a mechanistic blueprint for homodimeric class I cytokine receptor activation and its dysregulation by individual mutations.
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Affiliation(s)
- Stephan Wilmes
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Maximillian Hafer
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Joni Vuorio
- Department of Physics, University of Helsinki, Helsinki, Finland
- Computational Physics Laboratory, Tampere University, Tampere, Finland
| | - Julie A Tucker
- York Biomedical Research Institute and Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Hauke Winkelmann
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Sara Löchte
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Tess A Stanly
- York Biomedical Research Institute and Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Katiuska D Pulgar Prieto
- York Biomedical Research Institute and Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Chetan Poojari
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Vivek Sharma
- Department of Physics, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Christian P Richter
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Rainer Kurre
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Stevan R Hubbard
- Skirball Institute and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Molecular and Cellular Physiology and Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ignacio Moraga
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, Helsinki, Finland.
- Computational Physics Laboratory, Tampere University, Tampere, Finland
| | - Ian S Hitchcock
- York Biomedical Research Institute and Department of Biology, University of York, Heslington, York YO10 5DD, UK.
| | - Jacob Piehler
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany.
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Disorders of FZ-CRD; insights towards FZ-CRD folding and therapeutic landscape. Mol Med 2019; 26:4. [PMID: 31892318 PMCID: PMC6938638 DOI: 10.1186/s10020-019-0129-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 12/13/2019] [Indexed: 02/08/2023] Open
Abstract
The ER is hub for protein folding. Proteins that harbor a Frizzled cysteine-rich domain (FZ-CRD) possess 10 conserved cysteine motifs held by a unique disulfide bridge pattern which attains a correct fold in the ER. Little is known about implications of disease-causing missense mutations within FZ-CRD families. Mutations in FZ-CRD of Frizzled class receptor 4 (FZD4) and Muscle, skeletal, receptor tyrosine kinase (MuSK) and Receptor tyrosine kinase-like orphan receptor 2 (ROR2) cause Familial Exudative Vitreoretinopathy (FEVR), Congenital Myasthenic Syndrome (CMS), and Robinow Syndrome (RS) respectively. We highlight reported pathogenic inherited missense mutations in FZ-CRD of FZD4, MuSK and ROR2 which misfold, and traffic abnormally in the ER, with ER-associated degradation (ERAD) as a common pathogenic mechanism for disease. Our review shows that all studied FZ-CRD mutants of RS, FEVR and CMS result in misfolded proteins and/or partially misfolded proteins with an ERAD fate, thus we coin them as “disorders of FZ-CRD”. Abnormal trafficking was demonstrated in 17 of 29 mutants studied; 16 mutants were within and/or surrounding the FZ-CRD with two mutants distant from FZ-CRD. These ER-retained mutants were improperly N-glycosylated confirming ER-localization. FZD4 and MuSK mutants were tagged with polyubiquitin chains confirming targeting for proteasomal degradation. Investigating the cellular and molecular mechanisms of these mutations is important since misfolded protein and ER-targeted therapies are in development. The P344R-MuSK kinase mutant showed around 50% of its in-vitro autophosphorylation activity and P344R-MuSK increased two-fold on proteasome inhibition. M105T-FZD4, C204Y-FZD4, and P344R-MuSK mutants are thermosensitive and therefore, might benefit from extending the investigation to a larger number of chemical chaperones and/or proteasome inhibitors. Nonetheless, FZ-CRD ER-lipidation it less characterized in the literature and recent structural data sheds light on the importance of lipidation in protein glycosylation, proper folding, and ER trafficking. Current treatment strategies in-place for the conformational disease landscape is highlighted. From this review, we envision that disorders of FZ-CRD might be receptive to therapies that target FZ-CRD misfolding, regulation of fatty acids, and/or ER therapies; thus paving the way for a newly explored paradigm to treat different diseases with common defects.
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Campos LW, Pissinato LG, Yunes JA. Deleterious and Oncogenic Mutations in the IL7RA. Cancers (Basel) 2019; 11:cancers11121952. [PMID: 31817502 PMCID: PMC6966522 DOI: 10.3390/cancers11121952] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 11/29/2019] [Accepted: 11/30/2019] [Indexed: 12/27/2022] Open
Abstract
Interleukin 7 (IL-7) is a critical cytokine that plays a fundamental role in B- and T-cell development and in acute lymphoblastic leukemia (ALL). Its receptor (IL7R) is a transmembrane heterodimer formed by the IL7Rα and the IL2Rγ chain (γc). The IL7R signals through the JAK/STAT pathway. Loss-of-function mutations and some polymorphisms of the IL7Rα were associated to immunodeficiency and inflammatory diseases, respectively. Gain-of-function mutations were described in T-cell ALL and in high risk precursor B-cell ALL. Most confirmed loss-of-function mutations occur in the extracellular part of the IL7Rα while oncogenic mutations are exclusively found in the extracellular juxtamembrane (EJM) or transmembrane regions. Oncogenic mutations promote either IL7Rα/IL7Rα homodimerization and constitutive signaling, or increased affinity to γc or IL-7. This work presents a review on IL7Rα polymorphisms/mutations and attempts to present a classification based on their structural consequences and resulting biological activity.
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Affiliation(s)
- Lívia Weijenborg Campos
- Centro Infantil Boldrini, Campinas, SP 13083-210, Brazil; (L.W.C.); (L.G.P.)
- Graduate Program in Genetics and Molecular Biology, State University of Campinas, Campinas, SP 13083-210, Brazil
| | - Leonardo Granato Pissinato
- Centro Infantil Boldrini, Campinas, SP 13083-210, Brazil; (L.W.C.); (L.G.P.)
- Graduate Program in Genetics and Molecular Biology, State University of Campinas, Campinas, SP 13083-210, Brazil
| | - José Andrés Yunes
- Centro Infantil Boldrini, Campinas, SP 13083-210, Brazil; (L.W.C.); (L.G.P.)
- Medical Genetics Department, Faculty of Medical Sciences, State University of Campinas, Campinas, SP 13083-894, Brazil
- Correspondence: ; Tel.: +55-19-37875070; Fax: +55-19-3289-3571
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20
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Martinez-Fabregas J, Wilmes S, Wang L, Hafer M, Pohler E, Lokau J, Garbers C, Cozzani A, Fyfe PK, Piehler J, Kazemian M, Mitra S, Moraga I. Kinetics of cytokine receptor trafficking determine signaling and functional selectivity. eLife 2019; 8:e49314. [PMID: 31774398 PMCID: PMC6914340 DOI: 10.7554/elife.49314] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 11/24/2019] [Indexed: 12/27/2022] Open
Abstract
Cytokines activate signaling via assembly of cell surface receptors, but it is unclear whether modulation of cytokine-receptor binding parameters can modify biological outcomes. We have engineered IL-6 variants with different affinities to gp130 to investigate how cytokine receptor binding dwell-times influence functional selectivity. Engineered IL-6 variants showed a range of signaling amplitudes and induced biased signaling, with changes in receptor binding dwell-times affecting more profoundly STAT1 than STAT3 phosphorylation. We show that this differential signaling arises from defective translocation of ligand-gp130 complexes to the endosomal compartment and competitive STAT1/STAT3 binding to phospho-tyrosines in gp130, and results in unique patterns of STAT3 binding to chromatin. This leads to a graded gene expression response and differences in ex vivo differentiation of Th17, Th1 and Treg cells. These results provide a molecular understanding of signaling biased by cytokine receptors, and demonstrate that manipulation of signaling thresholds is a useful strategy to decouple cytokine functional pleiotropy.
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Affiliation(s)
- Jonathan Martinez-Fabregas
- Division of Cell Signaling and Immunology, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
| | - Stephan Wilmes
- Division of Cell Signaling and Immunology, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
| | - Luopin Wang
- Department Computer SciencePurdue UniversityWest LafayetteUnited States
| | | | - Elizabeth Pohler
- Division of Cell Signaling and Immunology, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
| | - Juliane Lokau
- Department of Pathology, Medical FacultyOtto-von-Guericke-University MagdeburgMagdeburgGermany
| | - Christoph Garbers
- Department of Pathology, Medical FacultyOtto-von-Guericke-University MagdeburgMagdeburgGermany
| | - Adeline Cozzani
- INSERM UMR-S-11721, Centre de Recherche Jean-Pierre Aubert (JPARC), Institut pour la Recherche sur le Cancer de Lille (IRCL), Université de LilleLilleFrance
| | - Paul K Fyfe
- Division of Cell Signaling and Immunology, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
| | - Jacob Piehler
- Department of BiologyUniversity of OsnabrückOsnabrückGermany
| | - Majid Kazemian
- Department Computer SciencePurdue UniversityWest LafayetteUnited States
| | - Suman Mitra
- INSERM UMR-S-11721, Centre de Recherche Jean-Pierre Aubert (JPARC), Institut pour la Recherche sur le Cancer de Lille (IRCL), Université de LilleLilleFrance
| | - Ignacio Moraga
- Division of Cell Signaling and Immunology, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
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Dey A, Barik D. Dichotomous Nature of Bistability Generated by Negative Cooperativity in Receptor-Ligand Binding. ACS Synth Biol 2019; 8:1294-1302. [PMID: 31132851 DOI: 10.1021/acssynbio.8b00517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Positive cooperativity in receptor-ligand binding plays an important role in cell signaling as it generates an ultrasensitive response, a requirement for nonlinear phenomena such as bistability and oscillations in feedback regulated reaction networks. On the other hand, negative cooperativity typically produces a hyperbolic response and is thus less explored. However, recently negative cooperativity was shown to generate an ultrasensitive response under the condition of strong ligand affinity. In this work, we have used mathematical modeling to investigate the effect of negative cooperativity in receptor-ligand interaction on the bistability in a positive feedback regulatory motif. We systematically investigated the effect of negative cooperativity, modifying the two equilibrium constants of the receptor-ligand binding, on the robustness and tunability of bistability. We show that in the regime where negative cooperativity exhibits robust bistability, positive cooperativity results in poor bistability and vice versa. Further we find that the robustness and tunability of bistability depend crucially on the stability of singly and doubly engaged receptors. Our modeling highlights the ability of negative cooperativity to produce complex phenomena with potential applications in designing synthetic devices or in explaining experimental observations in cell biology.
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Affiliation(s)
- Anupam Dey
- School of Chemistry, University of Hyderabad, Central University
P.O., Hyderabad, 500046 Telangana, India
| | - Debashis Barik
- School of Chemistry, University of Hyderabad, Central University
P.O., Hyderabad, 500046 Telangana, India
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22
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Mohan K, Ueda G, Kim AR, Jude KM, Fallas JA, Guo Y, Hafer M, Miao Y, Saxton RA, Piehler J, Sankaran VG, Baker D, Garcia KC. Topological control of cytokine receptor signaling induces differential effects in hematopoiesis. Science 2019; 364:eaav7532. [PMID: 31123111 PMCID: PMC7274355 DOI: 10.1126/science.aav7532] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/08/2019] [Indexed: 12/13/2022]
Abstract
Although tunable signaling by G protein-coupled receptors can be exploited through medicinal chemistry, a comparable pharmacological approach has been lacking for the modulation of signaling through dimeric receptors, such as those for cytokines. We present a strategy to modulate cytokine receptor signaling output by use of a series of designed C2-symmetric cytokine mimetics, based on the designed ankyrin repeat protein (DARPin) scaffold, that can systematically control erythropoietin receptor (EpoR) dimerization orientation and distance between monomers. We sampled a range of EpoR geometries by varying intermonomer angle and distance, corroborated by several ligand-EpoR complex crystal structures. Across the range, we observed full, partial, and biased agonism as well as stage-selective effects on hematopoiesis. This surrogate ligand strategy opens access to pharmacological modulation of therapeutically important cytokine and growth factor receptor systems.
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Affiliation(s)
- Kritika Mohan
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - George Ueda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Ah Ram Kim
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin M Jude
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jorge A Fallas
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Yu Guo
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
| | - Maximillian Hafer
- Division of Biophysics, Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Yi Miao
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Robert A Saxton
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jacob Piehler
- Division of Biophysics, Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
- Center for Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Vijay G Sankaran
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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23
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Emerging technologies in protein interface engineering for biomedical applications. Curr Opin Biotechnol 2019; 60:82-88. [PMID: 30802788 DOI: 10.1016/j.copbio.2019.01.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/26/2018] [Accepted: 01/21/2019] [Indexed: 12/27/2022]
Abstract
Protein interactions communicate critical information from the environment into cells to orchestrate functional responses relevant to health and disease. Whereas the natural repertoire of protein interfaces is finite, biomolecular engineering tools provide access to an unlimited scope of potential interactions that can be custom-designed for affinity, specificity, mechanism, or other properties of interest. This review highlights recent developments in protein interface engineering that offer insight into human physiology to inform the design of new pharmaceuticals, with a particular focus on immunotherapeutics. We cover three innovative and translationally promising approaches: (1) reprogramming receptor oligomerization to manipulate signaling pathways; (2) computational protein interface design strategies; and (3) engineering bioorthogonal protein interaction networks.
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24
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Yang H, Kureshi R, Spangler JB. Structural Basis for Signaling Through Shared Common γ Chain Cytokines. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1172:1-19. [PMID: 31628649 DOI: 10.1007/978-981-13-9367-9_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The common γ chain (γc) family of hematopoietic cytokines consists of six distinct four α-helix bundle soluble ligands that signal through receptors which include the shared γc subunit to coordinate a wide range of physiological processes, in particular, those related to innate and adaptive immune function. Since the first crystallographic structure of a γc family cytokine/receptor signaling complex (the active Interleukin-2 [IL-2] quaternary complex) was determined in 2005 [1], tremendous progress has been made in the structural characterization of this protein family, transforming our understanding of the molecular mechanisms underlying immune activity. Although many conserved features of γc family cytokine complex architecture have emerged, distinguishing details have been observed for individual cytokine complexes that rationalize their unique functional properties. Much work remains to be done in the molecular characterization of γc family signaling, particularly with regard to intracellular activation events, and looking forward, new technologies in structural biophysics will offer further insight into the biology of cytokine signaling to inform the design of targeted therapeutics for treatment of immune-linked diseases such as cancer, infection, and autoimmune disorders.
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Affiliation(s)
- Huilin Yang
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Rakeeb Kureshi
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jamie B Spangler
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA. .,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
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25
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Feng Y, Chen CS, Ho J, Pearce D, Hu S, Wang B, Desai P, Kim KS, Zhu H. High-Throughput Chip Assay for Investigating Escherichia coli Interaction with the Blood-Brain Barrier Using Microbial and Human Proteome Microarrays (Dual-Microarray Technology). Anal Chem 2018; 90:10958-10966. [PMID: 30106562 DOI: 10.1021/acs.analchem.8b02513] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bacterial meningitis in neonates and infants is an acute lethal disease and occurs in response to microbial exploitation of the blood-brain barrier (BBB), resulting in the intracranial inflammation. Several pathogens, such as Escherichia coli ( E. coli), can cause this devastating disease; however, the underlying molecular mechanisms by which these pathogens exploit the BBB remain incompletely understood. To identify important players on both the pathogen and host sides that govern the E. coli-BBB cell interactions, we took advantage of the E. coli and human proteome microarrays (i.e., HuProt) as an unbiased, proteome-wide tool for identification of important players on both sides. Using the E. coli proteome microarrays, we developed a unique high throughput chip-based cell probing assay to probe with fluorescent live human brain microvascular endothelial cells (HBMEC, which constitute the BBB). We identified several transmembrane proteins, which effectively bound to live HBMEC. We focused on YojI protein for further study. By probing the HuProt arrays with YojI, interferon-alpha receptor (IFNAR2) was identified as one of its binding proteins. The importance of YojI and IFNAR2 involved in E. coli-HBMEC interactions was characterized using the YojI knockout bacteria and IFNAR2-knock down HBMEC and further confirmed by E. coli binding assay in HBMEC. This study represents a new paradigm (dual-microarray technology) that enables rapid, unbiased discovery of both pathogen and host players that are involved in pathogen-host interactions for human infectious diseases in a high throughput manner.
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Affiliation(s)
- Yingzhu Feng
- Key Laboratory of Bio-theological Science and Technology of Ministry of Education, College of Bioengineering , Chongqing University , Chongqing 400030 , PR China.,Department of Pharmacology and Molecular Sciences, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States.,School of Life Sciences , Sun Yat-Sen University , Guangzhou 510275 , China
| | - Chien-Sheng Chen
- Department of Food Safety/Hygiene and Risk Management , Tainan City 701 , Taiwan.,Department of Pharmacology and Molecular Sciences, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States.,Department of Biomedical Science and Engineering , National Central University , Taoyuan City 32001 , Taiwan
| | - Jessica Ho
- Department of Pharmacology and Molecular Sciences, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States
| | - Donna Pearce
- Division of Pediatric Infectious Diseases, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21287 , United States
| | - Shaohui Hu
- Department of Pharmacology and Molecular Sciences, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States
| | - Bochu Wang
- Key Laboratory of Bio-theological Science and Technology of Ministry of Education, College of Bioengineering , Chongqing University , Chongqing 400030 , PR China
| | - Prashant Desai
- The Sidney Kimmel Comprehensive Cancer Center, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21231 , United States
| | - Kwang Sik Kim
- Division of Pediatric Infectious Diseases, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21287 , United States
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States
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26
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Spangler JB, Trotta E, Tomala J, Peck A, Young TA, Savvides CS, Silveria S, Votavova P, Salafsky J, Pande VS, Kovar M, Bluestone JA, Garcia KC. Engineering a Single-Agent Cytokine/Antibody Fusion That Selectively Expands Regulatory T Cells for Autoimmune Disease Therapy. THE JOURNAL OF IMMUNOLOGY 2018; 201:2094-2106. [PMID: 30104245 DOI: 10.4049/jimmunol.1800578] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/19/2018] [Indexed: 12/18/2022]
Abstract
IL-2 has been used to treat diseases ranging from cancer to autoimmune disorders, but its concurrent immunostimulatory and immunosuppressive effects hinder efficacy. IL-2 orchestrates immune cell function through activation of a high-affinity heterotrimeric receptor (composed of IL-2Rα, IL-2Rβ, and common γ [γc]). IL-2Rα, which is highly expressed on regulatory T (TReg) cells, regulates IL-2 sensitivity. Previous studies have shown that complexation of IL-2 with the JES6-1 Ab preferentially biases cytokine activity toward TReg cells through a unique mechanism whereby IL-2 is exchanged from the Ab to IL-2Rα. However, clinical adoption of a mixed Ab/cytokine complex regimen is limited by stoichiometry and stability concerns. In this study, through structure-guided design, we engineered a single agent fusion of the IL-2 cytokine and JES6-1 Ab that, despite being covalently linked, preserves IL-2 exchange, selectively stimulating TReg expansion and exhibiting superior disease control to the mixed IL-2/JES6-1 complex in a mouse colitis model. These studies provide an engineering blueprint for resolving a major barrier to the implementation of functionally similar IL-2/Ab complexes for treatment of human disease.
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Affiliation(s)
- Jamie B Spangler
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Eleonora Trotta
- Diabetes Center, University of California San Francisco, San Francisco, CA 94143
| | - Jakub Tomala
- Laboratory of Tumor Immunology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, 14220 Prague 4-Krc, Czech Republic
| | - Ariana Peck
- Department of Biochemistry, Stanford University, Stanford, CA 94305
| | | | | | - Stephanie Silveria
- Diabetes Center, University of California San Francisco, San Francisco, CA 94143
| | - Petra Votavova
- Laboratory of Tumor Immunology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, 14220 Prague 4-Krc, Czech Republic
| | | | - Vijay S Pande
- Department of Bioengineering, Stanford University, Stanford, CA 94305; and
| | - Marek Kovar
- Laboratory of Tumor Immunology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, 14220 Prague 4-Krc, Czech Republic
| | - Jeffrey A Bluestone
- Diabetes Center, University of California San Francisco, San Francisco, CA 94143.,Sean N. Parker Autoimmune Research Laboratory, University of California San Francisco, San Francisco, CA 94143
| | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305; .,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
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27
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Ligand-induced type II interleukin-4 receptor dimers are sustained by rapid re-association within plasma membrane microcompartments. Nat Commun 2017; 8:15976. [PMID: 28706306 PMCID: PMC5519985 DOI: 10.1038/ncomms15976] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 05/16/2017] [Indexed: 12/14/2022] Open
Abstract
The spatiotemporal organization of cytokine receptors in the plasma membrane is still debated with models ranging from ligand-independent receptor pre-dimerization to ligand-induced receptor dimerization occurring only after receptor uptake into endosomes. Here, we explore the molecular and cellular determinants governing the assembly of the type II interleukin-4 receptor, taking advantage of various agonists binding the receptor subunits with different affinities and rate constants. Quantitative kinetic studies using artificial membranes confirm that receptor dimerization is governed by the two-dimensional ligand–receptor interactions and identify a critical role of the transmembrane domain in receptor dimerization. Single molecule localization microscopy at physiological cell surface expression levels, however, reveals efficient ligand-induced receptor dimerization by all ligands, largely independent of receptor binding affinities, in line with the similar STAT6 activation potencies observed for all IL-4 variants. Detailed spatiotemporal analyses suggest that kinetic trapping of receptor dimers in actin-dependent microcompartments sustains robust receptor dimerization and signalling. The contribution of ligands for cytokine receptor dimerization is still not fully understood. Here, the authors show the efficient ligand-induced dimerization of type II interleukin-4 receptor at the plasma membrane and the kinetic trapping of signalling complexes by actin-dependent membrane microdomains.
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28
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Ho CCM, Chhabra A, Starkl P, Schnorr PJ, Wilmes S, Moraga I, Kwon HS, Gaudenzio N, Sibilano R, Wehrman TS, Gakovic M, Sockolosky JT, Tiffany MR, Ring AM, Piehler J, Weissman IL, Galli SJ, Shizuru JA, Garcia KC. Decoupling the Functional Pleiotropy of Stem Cell Factor by Tuning c-Kit Signaling. Cell 2017; 168:1041-1052.e18. [PMID: 28283060 DOI: 10.1016/j.cell.2017.02.011] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 12/20/2016] [Accepted: 02/06/2017] [Indexed: 12/20/2022]
Abstract
Most secreted growth factors and cytokines are functionally pleiotropic because their receptors are expressed on diverse cell types. While important for normal mammalian physiology, pleiotropy limits the efficacy of cytokines and growth factors as therapeutics. Stem cell factor (SCF) is a growth factor that acts through the c-Kit receptor tyrosine kinase to elicit hematopoietic progenitor expansion but can be toxic when administered in vivo because it concurrently activates mast cells. We engineered a mechanism-based SCF partial agonist that impaired c-Kit dimerization, truncating downstream signaling amplitude. This SCF variant elicited biased activation of hematopoietic progenitors over mast cells in vitro and in vivo. Mouse models of SCF-mediated anaphylaxis, radioprotection, and hematopoietic expansion revealed that this SCF partial agonist retained therapeutic efficacy while exhibiting virtually no anaphylactic off-target effects. The approach of biasing cell activation by tuning signaling thresholds and outputs has applications to many dimeric receptor-ligand systems.
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Affiliation(s)
- Chia Chi M Ho
- Department of Bioengineering, Stanford University School of Engineering, 443 Via Ortega, Stanford, CA 94305, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Akanksha Chhabra
- Department of Blood and Marrow Transplantation, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Philipp Starkl
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Department of Medicine I, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Peter-John Schnorr
- Department of Blood and Marrow Transplantation, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Stephan Wilmes
- Department of Biology, University of Osnabruck, Barbarastr. 11, 49076 Osnabruck, Germany
| | - Ignacio Moraga
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA
| | - Hye-Sook Kwon
- Department of Blood and Marrow Transplantation, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Nicolas Gaudenzio
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
| | - Riccardo Sibilano
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
| | - Tom S Wehrman
- Primity Bio, 48383 Fremont Blvd, Suite 118, Fremont, CA 94538, USA
| | - Milica Gakovic
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA
| | - Jonathan T Sockolosky
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA
| | - Matthew R Tiffany
- Department of Pediatrics and Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
| | - Aaron M Ring
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, 299 Campus Drive, Stanford, CA 94305, USA
| | - Jacob Piehler
- Department of Biology, University of Osnabruck, Barbarastr. 11, 49076 Osnabruck, Germany
| | - Irving L Weissman
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA; Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Stephen J Galli
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, 299 Campus Drive, Stanford, CA 94305, USA
| | - Judith A Shizuru
- Department of Blood and Marrow Transplantation, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, 299 Campus Drive, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA.
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29
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Moraga I, Spangler JB, Mendoza JL, Gakovic M, Wehrman TS, Krutzik P, Garcia KC. Synthekines are surrogate cytokine and growth factor agonists that compel signaling through non-natural receptor dimers. eLife 2017; 6. [PMID: 28498099 PMCID: PMC5429090 DOI: 10.7554/elife.22882] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/14/2017] [Indexed: 12/22/2022] Open
Abstract
Cytokine and growth-factor ligands typically signal through homo- or hetero-dimeric cell surface receptors via Janus Kinase (JAK/TYK), or Receptor Tyrosine Kinase (RTK)-mediated trans-phosphorylation. However, the number of receptor dimer pairings occurring in nature is limited to those driven by natural ligands encoded within our genome. We have engineered synthethic cytokines (synthekines) that drive formation of cytokine receptor dimer pairings that are not formed by endogenous cytokines and that are not found in nature, and which activate distinct signaling programs. We show that a wide range of non-natural cytokine receptor hetero-dimers are competent to elicit a signaling output. We engineered synthekine ligands that assembled IL-2Rβ/IL-4Rα or IL-4Rα/IFNAR2 receptor heterodimers, that do not occur naturally, triggering signaling and functional responses distinct from those activated by the endogenous cytokines IL-2, IL-4, and IFN. Furthermore, hybrid synthekine ligands that dimerized a JAK/STAT cytokine receptor with a receptor tyrosine kinase (RTK) also elicited a signaling response. Synthekines represent a new family of synthetic ligands with pre-defined receptors, but 'orphan' functions, that enable the full combinatorial scope of dimeric signaling receptors encoded within the human genome to be exploited for basic research and drug discovery.
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Affiliation(s)
- Ignacio Moraga
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States.,Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Jamie B Spangler
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States.,Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Juan L Mendoza
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States.,Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Milica Gakovic
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States.,Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | | | | | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States.,Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
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30
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Chen PH, Yao H, Huang LJS. Cytokine Receptor Endocytosis: New Kinase Activity-Dependent and -Independent Roles of PI3K. Front Endocrinol (Lausanne) 2017; 8:78. [PMID: 28507533 PMCID: PMC5410625 DOI: 10.3389/fendo.2017.00078] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/30/2017] [Indexed: 12/14/2022] Open
Abstract
Type I and II cytokine receptors are cell surface sensors that bind cytokines in the extracellular environment and initiate intracellular signaling to control processes such as hematopoiesis, immune function, and cellular growth and development. One key mechanism that regulates signaling from cytokine receptors is through receptor endocytosis. In this mini-review, we describe recent advances in endocytic regulations of cytokine receptors, focusing on new paradigms by which PI3K controls receptor endocytosis through both kinase activity-dependent and -independent mechanisms. These advances underscore the notion that the p85 regulatory subunit of PI3K has functions beyond regulating PI3K kinase activity, and that PI3K plays both positive and negative roles in receptor signaling. On the one hand, the PI3K/Akt pathway controls various aspects downstream of cytokine receptors. On the other hand, it stimulates receptor endocytosis and downregulation, thus contributing to signaling attenuation.
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Affiliation(s)
- Ping-hung Chen
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Huiyu Yao
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lily Jun-shen Huang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- *Correspondence: Lily Jun-shen Huang,
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31
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Moraga I, Richter D, Wilmes S, Winkelmann H, Jude K, Thomas C, Suhoski MM, Engleman EG, Piehler J, Garcia KC. Instructive roles for cytokine-receptor binding parameters in determining signaling and functional potency. Sci Signal 2015; 8:ra114. [PMID: 26554818 DOI: 10.1126/scisignal.aab2677] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cytokines dimerize cell surface receptors to activate signaling and regulate many facets of the immune response. Many cytokines have pleiotropic effects, inducing a spectrum of redundant and distinct effects on different cell types. This pleiotropy has hampered cytokine-based therapies, and the high doses required for treatment often lead to off-target effects, highlighting the need for a more detailed understanding of the parameters controlling cytokine-induced signaling and bioactivities. Using the prototypical cytokine interleukin-13 (IL-13), we explored the interrelationships between receptor binding and a wide range of downstream cellular responses. We applied structure-based engineering to generate IL-13 variants that covered a spectrum of binding strengths for the receptor subunit IL-13Rα1. Engineered IL-13 variants representing a broad range of affinities for the receptor exhibited similar potencies in stimulating the phosphorylation of STAT6 (signal transducer and activator of transcription 6). Delays in the phosphorylation and nuclear translocation of STAT6 were only apparent for those IL-13 variants with markedly reduced affinities for the receptor. From these data, we developed a mechanistic model that quantitatively reproduced the kinetics of STAT6 phosphorylation for the entire spectrum of binding affinities. Receptor endocytosis played a key role in modulating STAT6 activation, whereas the lifetime of receptor-ligand complexes at the plasma membrane determined the potency of the variant for inducing more distal responses. This complex interrelationship between extracellular ligand binding and receptor function provides the foundation for new mechanism-based strategies that determine the optimal cytokine dose to enhance therapeutic efficacy.
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Affiliation(s)
- Ignacio Moraga
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305-5345, USA. Department of Molecular and Cellular Physiology and Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5345, USA
| | - David Richter
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Stephan Wilmes
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Hauke Winkelmann
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Kevin Jude
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305-5345, USA. Department of Molecular and Cellular Physiology and Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5345, USA
| | - Christoph Thomas
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305-5345, USA. Department of Molecular and Cellular Physiology and Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5345, USA
| | - Megan M Suhoski
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305-5345, USA
| | - Edgar G Engleman
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305-5345, USA
| | - Jacob Piehler
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany.
| | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305-5345, USA. Department of Molecular and Cellular Physiology and Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5345, USA.
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Moraga I, Wernig G, Wilmes S, Gryshkova V, Richter CP, Hong WJ, Sinha R, Guo F, Fabionar H, Wehrman TS, Krutzik P, Demharter S, Plo I, Weissman IL, Minary P, Majeti R, Constantinescu SN, Piehler J, Garcia KC. Tuning cytokine receptor signaling by re-orienting dimer geometry with surrogate ligands. Cell 2015; 160:1196-208. [PMID: 25728669 PMCID: PMC4766813 DOI: 10.1016/j.cell.2015.02.011] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 01/22/2015] [Accepted: 02/03/2015] [Indexed: 01/07/2023]
Abstract
Most cell-surface receptors for cytokines and growth factors signal as dimers, but it is unclear whether remodeling receptor dimer topology is a viable strategy to "tune" signaling output. We utilized diabodies (DA) as surrogate ligands in a prototypical dimeric receptor-ligand system, the cytokine Erythropoietin (EPO) and its receptor (EpoR), to dimerize EpoR ectodomains in non-native architectures. Diabody-induced signaling amplitudes varied from full to minimal agonism, and structures of these DA/EpoR complexes differed in EpoR dimer orientation and proximity. Diabodies also elicited biased or differential activation of signaling pathways and gene expression profiles compared to EPO. Non-signaling diabodies inhibited proliferation of erythroid precursors from patients with a myeloproliferative neoplasm due to a constitutively active JAK2V617F mutation. Thus, intracellular oncogenic mutations causing ligand-independent receptor activation can be counteracted by extracellular ligands that re-orient receptors into inactive dimer topologies. This approach has broad applications for tuning signaling output for many dimeric receptor systems.
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Affiliation(s)
- Ignacio Moraga
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Gerlinde Wernig
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Department of Pathology, Division of Hematopathology, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Stephan Wilmes
- Division of Biophysics, Department of Biology, University of Osnabrück, 49076, Germany
| | - Vitalina Gryshkova
- Ludwig Institute For Cancer Research and de Duve Institute, Université catholique de Louvain, B-1200 Brussels, Belgium
| | | | - Wan-Jen Hong
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Department of Internal Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Feng Guo
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Hyna Fabionar
- DiscoveRx, 42501 Albrae St, Fremont, California, 94538, USA
| | - Tom S. Wehrman
- Primity Bio, 3350 Scott blvd ste 6101, Santa Clara, CA 95054
| | - Peter Krutzik
- Primity Bio, 3350 Scott blvd ste 6101, Santa Clara, CA 95054
| | - Samuel Demharter
- Department of Computer Science Wolfson Building, University of Oxford, Oxford OX1 3QD, United Kingdom
| | - Isabelle Plo
- Institut Gustave Roussy, INSERM U1009, 94805, Villejuif, France
| | - Irving L. Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Peter Minary
- Department of Computer Science Wolfson Building, University of Oxford, Oxford OX1 3QD, United Kingdom
| | - Ravindra Majeti
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Department of Internal Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Stefan N. Constantinescu
- Ludwig Institute For Cancer Research and de Duve Institute, Université catholique de Louvain, B-1200 Brussels, Belgium
| | - Jacob Piehler
- Division of Biophysics, Department of Biology, University of Osnabrück, 49076, Germany
| | - K. Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Correspondence to:
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33
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The molecular basis for functional plasticity in type I interferon signaling. Trends Immunol 2015; 36:139-49. [DOI: 10.1016/j.it.2015.01.002] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/13/2015] [Accepted: 01/13/2015] [Indexed: 01/16/2023]
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Spangler JB, Moraga I, Mendoza JL, Garcia KC. Insights into cytokine-receptor interactions from cytokine engineering. Annu Rev Immunol 2014; 33:139-67. [PMID: 25493332 DOI: 10.1146/annurev-immunol-032713-120211] [Citation(s) in RCA: 180] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cytokines exert a vast array of immunoregulatory actions critical to human biology and disease. However, the desired immunotherapeutic effects of native cytokines are often mitigated by toxicity or lack of efficacy, either of which results from cytokine receptor pleiotropy and/or undesired activation of off-target cells. As our understanding of the structural principles of cytokine-receptor interactions has advanced, mechanism-based manipulation of cytokine signaling through protein engineering has become an increasingly feasible and powerful approach. Modified cytokines, both agonists and antagonists, have been engineered with narrowed target cell specificities, and they have also yielded important mechanistic insights into cytokine biology and signaling. Here we review the theory and practice of cytokine engineering and rationalize the mechanisms of several engineered cytokines in the context of structure. We discuss specific examples of how structure-based cytokine engineering has opened new opportunities for cytokines as drugs, with a focus on the immunotherapeutic cytokines interferon, interleukin-2, and interleukin-4.
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Affiliation(s)
- Jamie B Spangler
- Howard Hughes Medical Institute, Department of Molecular and Cellular Physiology, Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305; , , ,
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Moraga I, Spangler J, Mendoza JL, Garcia KC. Multifarious determinants of cytokine receptor signaling specificity. Adv Immunol 2014; 121:1-39. [PMID: 24388212 DOI: 10.1016/b978-0-12-800100-4.00001-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cytokines play crucial roles in regulating immune homeostasis. Two important characteristics of most cytokines are pleiotropy, defined as the ability of one cytokine to exhibit diverse functionalities, and redundancy, defined as the ability of multiple cytokines to exert overlapping activities. Identifying the determinants for unique cellular responses to cytokines in the face of shared receptor usage, pleiotropy, and redundancy will be essential in order to harness the potential of cytokines as therapeutics. Here, we discuss the biophysical (ligand-receptor geometry and affinity) and cellular (receptor trafficking and intracellular abundance of signaling molecules) parameters that contribute to the specificity of cytokine bioactivities. Whereas the role of extracellular ternary complex geometry in cytokine-induced signaling is still not completely elucidated, cytokine-receptor affinity is known to impact signaling through modulation of the stability and kinetics of ternary complex formation. Receptor trafficking also plays an important and likely underappreciated role in the diversification of cytokine bioactivities but it has been challenging to experimentally probe trafficking effects. We also review recent efforts to quantify levels of intracellular signaling components, as second messenger abundance can affect cytokine-induced bioactivities both quantitatively and qualitatively. We conclude by discussing the application of protein engineering to develop therapeutically relevant cytokines with reduced pleiotropy and redirected biological functionalities.
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Affiliation(s)
- Ignacio Moraga
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA; Program in Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Jamie Spangler
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA; Program in Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Juan L Mendoza
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA; Program in Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA; Program in Immunology, Stanford University School of Medicine, Stanford, California, USA.
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36
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Sedek M, van der Velden LM, Strous GJ. Multimeric growth hormone receptor complexes serve as signaling platforms. J Biol Chem 2013; 289:65-73. [PMID: 24280222 DOI: 10.1074/jbc.m113.523373] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Growth hormone (GH) signaling is required for promoting longitudinal body growth, stem cell activation, differentiation, and survival and for regulation of metabolism. Failure to adequately regulate GH signaling leads to disease: excessive GH signaling has been connected to cancer, and GH insensitivity has been reported in cachexia patients. Since its discovery in 1989, the receptor has served a pivotal role as the prototype cytokine receptor both structurally and functionally. Phosphorylation and ubiquitylation regulate the GH receptor (GHR) at the cell surface: two ubiquitin ligases (SCF(βTrCP2) and CHIP) determine the GH responsiveness of cells by controlling its endocytosis, whereas JAK2 initiates the JAK/STAT pathway. We used blue native electrophoresis to identify phosphorylated and ubiquitylated receptor intermediates. We show that GHRs occur as ∼500-kDa complexes that dimerize into active ∼900-kDa complexes upon GH binding. The dimerized complexes act as platforms for transient interaction with JAK2 and ubiquitin ligases. If GH and receptors are made in the same cell (autocrine mode), only limited numbers of ∼900-kDa complexes are formed. The experiments reveal the dynamic changes in post-translational modifications during GH-induced signaling events and show that relatively simple cytokine receptors like GHRs are able to form higher order protein complexes. Insight in the complex formation of cytokine receptors is crucially important for engineering cytokines that control ligand-induced cell responses and for generating a new class of therapeutic agents for a wide range of diseases.
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Affiliation(s)
- Magdalena Sedek
- From the Department of Cell Biology and Institute of Biomembranes, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
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37
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Yewale C, Baradia D, Vhora I, Patil S, Misra A. Epidermal growth factor receptor targeting in cancer: a review of trends and strategies. Biomaterials 2013; 34:8690-707. [PMID: 23953842 DOI: 10.1016/j.biomaterials.2013.07.100] [Citation(s) in RCA: 353] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 07/28/2013] [Indexed: 01/03/2023]
Abstract
The epidermal growth factor receptor (EGFR) is a cell-surface receptor belonging to ErbB family of tyrosine kinase and it plays a vital role in the regulation of cell proliferation, survival and differentiation. However; EGFR is aberrantly activated by various mechanisms like receptor overexpression, mutation, ligand-dependent receptor dimerization, ligand-independent activation and is associated with development of variety of tumors. Therefore, specific EGFR inhibition is one of the key targets for cancer therapy. Two major approaches have been developed and demonstrated benefits in clinical trials for targeting EGFR; monoclonal antibodies (mAbs) and tyrosine kinase inhibitors (TKIs). EGFR inhibitors like, cetuximab, panitumumab, etc. (mAbs) and gefitinib, erlotinib, lapatinib, etc. (TKIs) are now commercially available for treatment of variety of cancers. Recently, many other agents like peptides, nanobodies, affibodies and antisense oligonucleotide have also shown better efficacy in targeting and inhibiting EGFR. Now a days, efforts are being focused to identify molecular markers that can predict patients more likely to respond to anti-EGFR therapy; to find out combinatorial approaches with EGFR inhibitors and to bring new therapeutic agents with clinical efficacy. In this review we have outlined the role of EGFR in cancer, different types of EGFR inhibitors, preclinical and clinical status of EGFR inhibitors as well as summarized the recent efforts made in the field of molecular EGFR targeting.
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Affiliation(s)
- Chetan Yewale
- Pharmacy Department, Faculty of Technology & Engineering, The Maharaja Sayajirao University of Baroda, Kalabhavan, Vadodara 390 001, Gujarat, India
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39
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Junttila IS, Creusot RJ, Moraga I, Bates DL, Wong MT, Alonso MN, Suhoski MM, Lupardus P, Meier-Schellersheim M, Engleman EG, Utz PJ, Fathman CG, Paul WE, Garcia KC. Redirecting cell-type specific cytokine responses with engineered interleukin-4 superkines. Nat Chem Biol 2012; 8:990-8. [PMID: 23103943 PMCID: PMC3508151 DOI: 10.1038/nchembio.1096] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 09/20/2012] [Indexed: 01/28/2023]
Abstract
Cytokines dimerize their receptors, with the binding of the 'second chain' triggering signaling. In the interleukin (IL)-4 and IL-13 system, different cell types express varying numbers of alternative second receptor chains (γc or IL-13Rα1), forming functionally distinct type I or type II complexes. We manipulated the affinity and specificity of second chain recruitment by human IL-4. A type I receptor-selective IL-4 'superkine' with 3,700-fold higher affinity for γc was three- to ten-fold more potent than wild-type IL-4. Conversely, a variant with high affinity for IL-13Rα1 more potently activated cells expressing the type II receptor and induced differentiation of dendritic cells from monocytes, implicating the type II receptor in this process. Superkines showed signaling advantages on cells with lower second chain numbers. Comparative transcriptional analysis reveals that the superkines induce largely redundant gene expression profiles. Variable second chain numbers can be exploited to redirect cytokines toward distinct cell subsets and elicit new actions, potentially improving the selectivity of cytokine therapy.
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Affiliation(s)
- Ilkka S. Junttila
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
- School of Medicine, University of Tampere, 33014, Tampere, Finland
- Fimlab Laboratories, Pirkanmaa Hospital District, 33521, Tampere, Finland
| | - Remi J. Creusot
- Department of Medicine, Division of Immunology & Rheumatology, Stanford University School of Medicine, Stanford, CA, 94305
| | - Ignacio Moraga
- Howard Hughes Medical Institute, Departments of Molecular and Cellular Physiology, Structural Biology, and Program in Immunology, Stanford University School of Medicine, Stanford, CA, 94305
| | - Darren L. Bates
- Howard Hughes Medical Institute, Departments of Molecular and Cellular Physiology, Structural Biology, and Program in Immunology, Stanford University School of Medicine, Stanford, CA, 94305
| | - Michael T. Wong
- Department of Medicine, Division of Immunology & Rheumatology, Stanford University School of Medicine, Stanford, CA, 94305
| | - Michael N. Alonso
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305
| | - Megan M. Suhoski
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305
| | - Patrick Lupardus
- Howard Hughes Medical Institute, Departments of Molecular and Cellular Physiology, Structural Biology, and Program in Immunology, Stanford University School of Medicine, Stanford, CA, 94305
| | - Martin Meier-Schellersheim
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Edgar G. Engleman
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305
| | - Paul J. Utz
- Department of Medicine, Division of Immunology & Rheumatology, Stanford University School of Medicine, Stanford, CA, 94305
| | - C. Garrison Fathman
- Department of Medicine, Division of Immunology & Rheumatology, Stanford University School of Medicine, Stanford, CA, 94305
| | - William E. Paul
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - K. Christopher Garcia
- Howard Hughes Medical Institute, Departments of Molecular and Cellular Physiology, Structural Biology, and Program in Immunology, Stanford University School of Medicine, Stanford, CA, 94305
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40
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Abstract
Receptor tyrosine kinases (RTKs) exhibit basal tyrosine phosphorylation and activity in the absence of ligand stimulation, which has been attributed to the "leaky" nature of tyrosine kinase autoinhibition and stochastic collisions of receptors in the membrane bilayer. This basal phosphorylation does not produce a signal of sufficient amplitude and intensity to manifest in a biological response and hence is considered to be a passive, futile process that does not have any biological function. This paradigm has now been challenged by a study showing that the basal phosphorylation of RTKs is a physiologically relevant process that is actively inhibited by the intracellular adaptor protein growth factor receptor-bound 2 (Grb2) and serves to "prime" receptors for a rapid response to ligand stimulation. Grb2 is conventionally known for playing positive roles in RTK signaling. The discovery of a negative regulatory role for Grb2 reveals that this adaptor acts as a double-edged sword in the regulation of RTK signaling.
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Affiliation(s)
- Artur A Belov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
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41
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Atanasova M, Whitty A. Understanding cytokine and growth factor receptor activation mechanisms. Crit Rev Biochem Mol Biol 2012; 47:502-30. [PMID: 23046381 DOI: 10.3109/10409238.2012.729561] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Our understanding of the detailed mechanism of action of cytokine and growth factor receptors - and particularly our quantitative understanding of the link between structure, mechanism and function - lags significantly behind our knowledge of comparable functional protein classes such as enzymes, G protein-coupled receptors, and ion channels. In particular, it remains controversial whether such receptors are activated by a mechanism of ligand-induced oligomerization, versus a mechanism in which the ligand binds to a pre-associated receptor dimer or oligomer that becomes activated through subsequent conformational rearrangement. A major limitation to progress has been the relative paucity of methods for performing quantitative mechanistic experiments on unmodified receptors expressed at endogenous levels on live cells. In this article, we review the current state of knowledge on the activation mechanisms of cytokine and growth factor receptors, critically evaluate the evidence for and against the different proposed mechanisms, and highlight other key questions that remain unanswered. New approaches and techniques have led to rapid recent progress in this area, and the field is poised for major advances in the coming years which promise to revolutionize our understanding of this large and biologically and medically important class of receptors.
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Affiliation(s)
- Mariya Atanasova
- Department of Chemistry, Boston University, Boston, MA 02215, USA
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42
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Janda CY, Waghray D, Levin AM, Thomas C, Garcia KC. Structural basis of Wnt recognition by Frizzled. Science 2012; 337:59-64. [PMID: 22653731 DOI: 10.1126/science.1222879] [Citation(s) in RCA: 604] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Wnts are lipid-modified morphogens that play critical roles in development principally through engagement of Frizzled receptors. The 3.25 angstrom structure of Xenopus Wnt8 (XWnt8) in complex with mouse Frizzled-8 (Fz8) cysteine-rich domain (CRD) reveals an unusual two-domain Wnt structure, not obviously related to known protein folds, resembling a "hand" with "thumb" and "index" fingers extended to grasp the Fz8-CRD at two distinct binding sites. One site is dominated by a palmitoleic acid lipid group projecting from serine 187 at the tip of Wnt's thumb into a deep groove in the Fz8-CRD. In the second binding site, the conserved tip of Wnt's "index finger" forms hydrophobic amino acid contacts with a depression on the opposite side of the Fz8-CRD. The conservation of amino acids in both interfaces appears to facilitate ligand-receptor cross-reactivity, which has important implications for understanding Wnt's functional pleiotropy and for developing Wnt-based drugs for cancer and regenerative medicine.
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Affiliation(s)
- Claudia Y Janda
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
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43
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Structural insights into the extracellular assembly of the hematopoietic Flt3 signaling complex. Blood 2011; 118:60-8. [DOI: 10.1182/blood-2011-01-329532] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Abstract
The class III receptor tyrosine kinase (RTKIII) Fms-like tyrosine kinase receptor 3 (Flt3) and its cytokine ligand (FL) play central roles in hematopoiesis and the immune system, by establishing signaling cascades crucial for the development and homeostasis of hematopoietic progenitors and antigen-presenting dendritic cells. However, Flt3 is also one of the most frequently mutated receptors in hematologic malignancies and is currently a major prognostic factor and clinical target for acute myeloid leukemia. Here, we report the structural basis for the Flt3 ligand-receptor complex and unveil an unanticipated extracellular assembly unlike any other RTKIII/V complex characterized to date. FL induces dimerization of Flt3 via a remarkably compact binding epitope localized at the tip of extracellular domain 3 of Flt3, and it invokes a ternary complex devoid of homotypic receptor interactions. Comparisons of Flt3 with homologous receptors and available mutagenesis data for FL have allowed us to rationalize the unique features of the Flt3 extracellular assembly. Furthermore, thermodynamic dissection of complex formation points to a pronounced enthalpically driven binding event coupled to an entropic penalty. Together, our data suggest that the high-affinity Flt3:FL complex is driven in part by a single preformed binding epitope on FL reminiscent of a “lock-and-key” binding mode, thereby setting the stage for antagonist design.
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44
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Pepłowski L, Sikora M, Nowak W, Cieplak M. Molecular jamming--the cystine slipknot mechanical clamp in all-atom simulations. J Chem Phys 2011; 134:085102. [PMID: 21361557 DOI: 10.1063/1.3553801] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force peaks in the range of 1 nN. Such high force peaks should be due to forcing of a slip-loop through a cystine ring, i.e., by generating a cystine slipknot. The survey has been performed in a simple coarse grained model. Here, we perform all-atom steered molecular dynamics simulations on 15 cystine knot proteins and determine their resistance to stretching. In agreement with previous studies within a coarse grained structure based model, the level of resistance is found to be substantially higher than in proteins in which the mechanical clamp operates through shear. The large stretching forces arise through formation of the cystine slipknot mechanical clamp and the resulting steric jamming. We elucidate the workings of such a clamp in an atomic detail. We also study the behavior of five top strength proteins with the shear-based mechanostability in which no jamming is involved. We show that in the atomic model, the jamming state is relieved by moving one amino acid at a time and there is a choice in the selection of the amino acid that advances the first. In contrast, the coarse grained model also allows for a simultaneous passage of two amino acids.
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Affiliation(s)
- Lukasz Pepłowski
- Institute of Physics, Nicolaus Copernicus University, Torun, Poland
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Lupardus PJ, Skiniotis G, Rice AJ, Thomas C, Fischer S, Walz T, Garcia KC. Structural snapshots of full-length Jak1, a transmembrane gp130/IL-6/IL-6Rα cytokine receptor complex, and the receptor-Jak1 holocomplex. Structure 2011; 19:45-55. [PMID: 21220115 DOI: 10.1016/j.str.2010.10.010] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 09/25/2010] [Accepted: 10/31/2010] [Indexed: 11/28/2022]
Abstract
The shared cytokine receptor gp130 signals as a homodimer or heterodimer through activation of Janus kinases (Jaks) associated with the receptor intracellular domains. Here, we reconstitute, in parts and whole, the full-length gp130 homodimer in complex with the cytokine interleukin-6 (IL-6), its alpha receptor (IL-6Rα) and Jak1, for electron microscopy imaging. We find that the full-length gp130 homodimer complex has intimate interactions between the trans- and juxtamembrane segments of the two receptors, appearing to form a continuous connection between the extra- and intracellular regions. 2D averages and 3D reconstructions of full-length Jak1 reveal a three lobed structure comprising FERM-SH2, pseudokinase, and kinase modules possessing extensive intersegmental flexibility that likely facilitates allosteric activation. Single-particle imaging of the gp130/IL-6/IL-6Rα/Jak1 holocomplex shows Jak1 associated with the membrane proximal intracellular regions of gp130, abutting the would-be inner leaflet of the cell membrane. Jak1 association with gp130 is enhanced by the presence of a membrane environment.
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Affiliation(s)
- Patrick J Lupardus
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
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Machado-Neto JA, Traina F, Lazarini M, Campos PDM, Pagnano KBB, Lorand-Metze I, Costa FF, Saad STO. Screening for hotspot mutations in PI3K, JAK2, FLT3 and NPM1 in patients with myelodysplastic syndromes. Clinics (Sao Paulo) 2011; 66:793-9. [PMID: 21789382 PMCID: PMC3109377 DOI: 10.1590/s1807-59322011000500014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 02/11/2011] [Indexed: 12/28/2022] Open
Abstract
INTRODUCTION Myelodysplastic syndromes encompass a heterogeneous group of clonal hematopoietic stem cell disorders characterized by ineffective hematopoiesis, refractory cytopenia and a tendency to progress toward acute myeloid leukemia. The accumulation of genetic alterations is closely associated with the progression of myelodysplastic syndromes toward acute myeloid leukemia. OBJECTIVE To investigate the presence of mutations in the points most frequent for mutations (hotspot mutations) in phosphatidylinositol-3-kinase (PI3K), Janus kinase 2 (JAK2), FMS-like tyrosine kinase 3 (FLT3) and nucleophosmin (NPM1), which are involved in leukemia and other cancers, in a population of Brazilian MDS patients. METHODS Fifty-one myelodysplastic syndromes patients were included in the study. According to French-American-British classification, the patients were distributed as follows: 31 with refractory anemia, 8 with refractory anemia with ringed sideroblasts, 7 with refractory anemia with excess blasts, 3 with refractory anemia with excess blasts in transformation and 2 with chronic myelomonocytic leukemia. Bone marrow samples were obtained and screened for the presence of hotspot mutations using analysis based on amplification with the polymerase chain reaction, sequencing, fragment size polymorphisms or restriction enzyme digestion. All patients were screened for mutations at the time of diagnosis, and 5 patients were also screened at the time of disease progression. RESULTS These results show that hotspot mutations in the PI3K, JAK2, FLT3 and NPM1 genes are not common in MDS patients; nevertheless, JAK2 mutations may be present in myelodysplasia during disease progression. CONCLUSIONS These results show that hotspot mutations in the PI3K, JAK2, FLT3 and NPM1 genes are not common in MDS patients; nevertheless, JAK2 mutations may be present in myelodysplasia during disease progression.
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Helmreich EJ. Ways and means of coping with uncertainties of the relationship of the genetic blue print to protein structure and function in the cell. Cell Commun Signal 2010; 8:26. [PMID: 20849616 PMCID: PMC2954850 DOI: 10.1186/1478-811x-8-26] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 09/17/2010] [Indexed: 11/24/2022] Open
Abstract
As one of the disciplines of systems biology, proteomics is central to enabling the elucidation of protein function within the cell; furthermore, the question of how to deduce protein structure and function from the genetic readout has gained new significance. This problem is of particular relevance for proteins engaged in cell signalling. In dealing with this question, I shall critically comment on the reliability and predictability of transmission and translation of the genetic blue print into the phenotype, the protein. Based on this information, I will then evaluate the intentions and goals of today's proteomics and gene-networking and appraise their chances of success. Some of the themes commented on in this publication are explored in greater detail with particular emphasis on the historical roots of concepts and techniques in my forthcoming book, published in German: Von Molekülen zu Zellen. 100 Jahre experimentelle Biologie. Betrachtungen eines Biochemikers.
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Radhakrishnan ML, Tidor B. Cellular level models as tools for cytokine design. Biotechnol Prog 2010; 26:919-37. [PMID: 20568274 DOI: 10.1002/btpr.387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cytokines and growth factors are critical regulators that connect intracellular and extracellular environments through binding to specific cell-surface receptors. They regulate a wide variety of immunological, growth, and inflammatory response processes. The overall signal initiated by a population of cytokine molecules over long time periods is controlled by the subtle interplay of binding, signaling, and trafficking kinetics. Building on the work of others, we abstract a simple kinetic model that captures relevant features from cytokine systems as well as related growth factor systems. We explore a large range of potential biochemical behaviors, through systematic examination of the model's parameter space. Different rates for the same reaction topology lead to a dramatic range of biochemical network properties and outcomes. Evolution might productively explore varied and different portions of parameter space to create beneficial behaviors, and effective human therapeutic intervention might be achieved through altering network kinetic properties. Quantitative analysis of the results reveals the basis for tensions among a number of different network characteristics. For example, strong binding of cytokine to receptor can increase short-term receptor activation and signal initiation but decrease long-term signaling due to internalization and degradation. Further analysis reveals the role of specific biochemical processes in modulating such tensions. For instance, the kinetics of cytokine binding and receptor activation modulate whether ligand-receptor dissociation can generally occur before signal initiation or receptor internalization. Beyond analysis, the same models and model behaviors provide an important basis for the design of more potent cytokine therapeutics by providing insight into how binding kinetics affect ligand potency.
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Affiliation(s)
- Mala L Radhakrishnan
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139
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Akabayov SR, Biron Z, Lamken P, Piehler J, Anglister J. NMR mapping of the IFNAR1-EC binding site on IFNalpha2 reveals allosteric changes in the IFNAR2-EC binding site. Biochemistry 2010; 49:687-95. [PMID: 20047337 DOI: 10.1021/bi901313x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
All type I interferons (IFNs) bind to a common cell-surface receptor consisting of two subunits. IFNs initiate intracellular signal transduction cascades by simultaneous interaction with the extracellular domains of its receptor subunits, IFNAR1 and IFNAR2. In this study, we mapped the surface of IFNalpha2 interacting with the extracellular domain of IFNAR1 (IFNAR1-EC) by following changes in or the disappearance of the (1)H-(15)N TROSY-HSQC cross peaks of IFNalpha2 caused by the binding of the extracellular domain of IFNAR1 (IFNAR1-EC) to the binary complex of IFNalpha2 with IFNAR2-EC. The NMR study of the 89 kDa complex was conducted at pH 8 and 308 K using an 800 MHz spectrometer. IFNAR1 binding affected a total of 47 of 165 IFNalpha2 residues contained in two large patches on the face of the protein opposing the binding site for IFNAR2 and in a third patch located on the face containing the IFNAR2 binding site. The first two patches form the IFNAR1 binding site, and one of these matches the IFNAR1 binding site previously identified by site-directed mutagenesis. The third patch partially matches the IFNalpha2 binding site for IFNAR2-EC, indicating allosteric communication between the binding sites for the two receptor subunits.
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Affiliation(s)
- Sabine Ruth Akabayov
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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Rose T, Pillet AH, Lavergne V, Tamarit B, Lenormand P, Rousselle JC, Namane A, Thèze J. Interleukin-7 compartmentalizes its receptor signaling complex to initiate CD4 T lymphocyte response. J Biol Chem 2010; 285:14898-14908. [PMID: 20167604 DOI: 10.1074/jbc.m110.104232] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Interleukin (IL)-7 is a central cytokine that controls homeostasis of the CD4 T lymphocyte pool. Here we show on human primary cells that IL-7 binds to preassembled receptors made up of proprietary chain IL-7Ralpha and the common chain gammac shared with IL-2, -4, -9, -15, and -21 receptors. Upon IL-7 binding, both chains are driven in cholesterol- and sphingomyelin-rich rafts where associated signaling proteins Jak1, Jak3, STAT1, -3, and -5 are found to be phosphorylated. Meanwhile the IL-7.IL-7R complex interacts with the cytoskeleton that halts its diffusion as measured by single molecule fluorescence autocorrelated spectroscopy monitored by microimaging. Comparative immunoprecipitations of IL-7Ralpha signaling complex from non-stimulated and IL-7-stimulated cells confirmed recruitment of proteins such as STATs, but many others were also identified by mass spectrometry from two-dimensional gels. Among recruited proteins, two-thirds are involved in cytoskeleton and raft formation. Thus, early events leading to IL-7 signal transduction involve its receptor compartmentalization into membrane nanodomains and cytoskeleton recruitment.
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Affiliation(s)
- Thierry Rose
- Institut Pasteur, Unité d'Immunogénétique Cellulaire, Département Infection et Epidémiologie, Département d'Immunologie, Genopole, 25 rue du Dr Roux, 75724 Paris Cedex 15, France.
| | - Anne-Hélène Pillet
- Institut Pasteur, Unité d'Immunogénétique Cellulaire, Département Infection et Epidémiologie, Département d'Immunologie, Genopole, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Vincent Lavergne
- Institut Pasteur, Unité d'Immunogénétique Cellulaire, Département Infection et Epidémiologie, Département d'Immunologie, Genopole, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Blanche Tamarit
- Institut Pasteur, Unité d'Immunogénétique Cellulaire, Département Infection et Epidémiologie, Département d'Immunologie, Genopole, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Pascal Lenormand
- Plate-Forme Protéomique, Genopole, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
| | | | - Abdelkader Namane
- Plate-Forme Protéomique, Genopole, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Jacques Thèze
- Institut Pasteur, Unité d'Immunogénétique Cellulaire, Département Infection et Epidémiologie, Département d'Immunologie, Genopole, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
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