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Yamamoto R, Segawa R, Kato H, Niino Y, Sato T, Hiratsuka M, Hirasawa N. Identification of amino acids in transmembrane domains of mutated cytokine receptor-like factor 2 and interleukin-7 receptor α required for constitutive signal transduction. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184359. [PMID: 38862034 DOI: 10.1016/j.bbamem.2024.184359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/25/2024] [Accepted: 06/05/2024] [Indexed: 06/13/2024]
Abstract
Cytokine receptor-like factor 2 (CRLF2) and interleukin-7 receptor α (IL-7Rα) form a receptor for thymic stromal lymphopoietin (TSLP). A somatic mutation consisting of the substitution of five amino acids (SLLLL) in the transmembrane domain of CRLF2 with three amino acids, including glutamic acid, isoleucine, and methionine (insEIM), which has been identified in acute lymphocytic leukemia, causes the TSLP-independent dimerization with IL-7Rα and activation. However, the dimerization mechanism remains unclear. In this study, we examined the involvement of the amino acids in the transmembrane domains of EIM CRLF2 and IL-7Rα in TSLP-independent activation. HEK293 cells were transfected with vectors encoding CRLF2 and IL-7Rα, or their mutants, in which the amino acid of the transmembrane domain was replaced with alanine. STAT5 phosphorylation was detected using western blotting, and receptor dimerization was analyzed using the NanoBiT assay. The substitution of glutamic acid within the insEIM mutation for alanine failed to cause the STAT5 phosphorylation in the absence of TSLP. Moreover, the alanine substation of the specific leucine residues in the transmembrane domains of both CRLF2 and IL-7Rα abrogated the TSLP-independent signal transduction and dimerization. The mutation of IL-7Rα W264 partially reduced the phosphorylation of STAT5 without affecting receptor dimerization. These results suggest that the amino acids in the transmembrane domains of EIM CRLF2 and IL-7Rα play at least three possible functions: interaction through hydrogen bonds, hydrophobic interaction, and signal transduction. Our findings contribute to a better understanding of the function of the transmembrane domains of cytokine receptors in their dimerization and signal transduction.
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Affiliation(s)
- Rio Yamamoto
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Miyagi, Japan
| | - Ryosuke Segawa
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Miyagi, Japan
| | - Hiyori Kato
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Miyagi, Japan
| | - Yuya Niino
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Miyagi, Japan
| | - Takeshi Sato
- Division of Liberal Arts and Science, Kyoto Pharmaceutical University, 607-8414 Kyoto, Japan
| | - Masahiro Hiratsuka
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Miyagi, Japan
| | - Noriyasu Hirasawa
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Miyagi, Japan.
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Huynh PN, Cheng C. Spatial-temporal comparison of Eph/Ephrin gene expression in ocular lenses from aging and knockout mice. FRONTIERS IN OPHTHALMOLOGY 2024; 4:1410860. [PMID: 38984128 PMCID: PMC11182306 DOI: 10.3389/fopht.2024.1410860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/06/2024] [Indexed: 07/11/2024]
Abstract
Cataracts, defined as any opacity in the transparent ocular lens, remain the leading cause of blindness and visual impairment in the world; however, the etiology of this pathology is not fully understood. Studies in mice and humans have found that the EphA2 receptor and the ephrin-A5 ligand play important roles in maintaining lens homeostasis and transparency. However, due to the diversity of the family of Eph receptors and ephrin ligands and their promiscuous binding, identifying functional interacting partners remains a challenge. Previously, 12 of the 14 Ephs and 8 of 8 ephrins in mice were characterized to be expressed in the mouse lens. To further narrow down possible genes of interest in life-long lens homeostasis, we collected and separated the lens epithelium from the fiber cell mass and isolated RNA from each compartment in samples from young adult and middle-aged mice that were either wild-type, EphA2-/- (knockout), or ephrin-A5 -/- . Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was implemented to compare transcript levels of 33 Eph and ephrin gene variants in each tissue compartment. Our results show that, of the Eph and ephrin variants screened, 5 of 33 showed age-related changes, and 2 of 33 showed genotype-related changes in lens epithelium. In the isolated fibers, more dynamic gene expression changes were observed, in which 12 of 33 variants showed age-related changes, and 6 of 33 showed genotype-related changes. These data allow for a more informed decision in determining mechanistic leads in Eph-ephrin-mediated signaling in the lens.
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Affiliation(s)
- Peter N Huynh
- School of Optometry and Vision Science Program, Indiana University, Bloomington, IN, United States
| | - Catherine Cheng
- School of Optometry and Vision Science Program, Indiana University, Bloomington, IN, United States
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Wirth D, Özdemir E, Wimley WC, Pasquale EB, Hristova K. Transmembrane helix interactions regulate oligomerization of the receptor tyrosine kinase EphA2. J Biol Chem 2024; 300:107441. [PMID: 38838777 DOI: 10.1016/j.jbc.2024.107441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/07/2024] Open
Abstract
The transmembrane helices of receptor tyrosine kinases (RTKs) have been proposed to switch between two different dimeric conformations, one associated with the inactive RTK and the other with the active RTK. Furthermore, recent work has demonstrated that some full-length RTKs are associated with oligomers that are larger than dimers, raising questions about the roles of the TM helices in the assembly and function of these oligomers. Here we probe the roles of the TM helices in the stability of EphA2 RTK oligomers in the plasma membrane. We employ mutagenesis to evaluate the relevance of a published NMR dimeric structure of the isolated EphA2 TM helix in the context of the full-length EphA2 in the plasma membrane. We use two fluorescence methods, Förster Resonance Energy Transfer and Fluorescence Intensity Fluctuations spectrometry, which yield complementary information about the EphA2 oligomerization process. These studies reveal that the TM helix mutations affect the stability, structure, and size of EphA2 oligomers. However, the effects are multifaceted and point to a more complex role of the TM helix than the one expected from the "TM dimer switch" model.
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Affiliation(s)
- Daniel Wirth
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ece Özdemir
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - William C Wimley
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Elena B Pasquale
- Cancer Metabolism and Microenvironment Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland, USA.
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Liang LY, Geoghegan ND, Mlodzianoski M, Leis A, Whitehead LW, Surudoi MG, Young SN, Janes P, Shepherd D, Ghosal D, Rogers KL, Murphy JM, Lucet IS. Co-clustering of EphB6 and ephrinB1 in trans restrains cancer cell invasion. Commun Biol 2024; 7:461. [PMID: 38627519 PMCID: PMC11021433 DOI: 10.1038/s42003-024-06118-4] [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: 02/20/2024] [Accepted: 03/27/2024] [Indexed: 04/19/2024] Open
Abstract
EphB6 is an understudied ephrin receptor tyrosine pseudokinase that is downregulated in multiple types of metastatic cancers. Unlike its kinase-active counterparts which autophosphorylate and transmit signals upon intercellular interaction, little is known about how EphB6 functions in the absence of intrinsic kinase activity. Here, we unveil a molecular mechanism of cell-cell interaction driven by EphB6. We identify ephrinB1 as a cognate ligand of EphB6 and show that in trans interaction of EphB6 with ephrinB1 on neighboring cells leads to the formation of large co-clusters at the plasma membrane. These co-clusters exhibit a decreased propensity towards endocytosis, suggesting a unique characteristic for this type of cell-cell interaction. Using lattice light-sheet microscopy, 3D structured illumination microscopy and cryo-electron tomography techniques, we show that co-clustering of EphB6 and ephrinB1 promotes the formation of double-membrane tubular structures between cells. Importantly, we also demonstrate that these intercellular structures stabilize cell-cell adhesion, leading to a reduction in the invasive behavior of cancer cells. Our findings rationalize a role for EphB6 pseudokinase as a tumor suppressor when interacting with its ligands in trans.
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Affiliation(s)
- Lung-Yu Liang
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Niall D Geoghegan
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Michael Mlodzianoski
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Andrew Leis
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Lachlan W Whitehead
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Minglyanna G Surudoi
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Samuel N Young
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Peter Janes
- Olivia Newton-John Cancer Research Institute and La Trobe School of Cancer Medicine, Level 5, ONJ Centre, 145 Studley Rd, Heidelberg, VIC, 3084, Australia
| | - Doulin Shepherd
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Debnath Ghosal
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3052, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Kelly L Rogers
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - James M Murphy
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.
| | - Isabelle S Lucet
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3052, Australia.
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Pasquale EB. Eph receptors and ephrins in cancer progression. Nat Rev Cancer 2024; 24:5-27. [PMID: 37996538 PMCID: PMC11015936 DOI: 10.1038/s41568-023-00634-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 11/25/2023]
Abstract
Evidence implicating Eph receptor tyrosine kinases and their ephrin ligands (that together make up the 'Eph system') in cancer development and progression has been accumulating since the discovery of the first Eph receptor approximately 35 years ago. Advances in the past decade and a half have considerably increased the understanding of Eph receptor-ephrin signalling mechanisms in cancer and have uncovered intriguing new roles in cancer progression and drug resistance. This Review focuses mainly on these more recent developments. I provide an update on the different mechanisms of Eph receptor-ephrin-mediated cell-cell communication and cell autonomous signalling, as well as on the interplay of the Eph system with other signalling systems. I further discuss recent advances in elucidating how the Eph system controls tumour expansion, invasiveness and metastasis, supports cancer stem cells, and drives therapy resistance. In addition to functioning within cancer cells, the Eph system also mediates the reciprocal communication between cancer cells and cells of the tumour microenvironment. The involvement of the Eph system in tumour angiogenesis is well established, but recent findings also demonstrate roles in immune cells, cancer-associated fibroblasts and the extracellular matrix. Lastly, I discuss strategies under evaluation for therapeutic targeting of Eph receptors-ephrins in cancer and conclude with an outlook on promising future research directions.
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Affiliation(s)
- Elena B Pasquale
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
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Ruiz-Padilla A, Turina M, Ayllón MA. Molecular characterization of a tetra segmented ssDNA virus infecting Botrytis cinerea worldwide. Virol J 2023; 20:306. [PMID: 38114992 PMCID: PMC10731770 DOI: 10.1186/s12985-023-02256-z] [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: 07/25/2023] [Accepted: 12/02/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Family Genomoviridae was recently established, and only a few mycoviruses have been described and characterized, and almost all of them (Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1, Fusarium graminearum gemyptripvirus 1 and Botrytis cinerea gemydayirivirus 1) induced hypovirulence in their host. Botrytis cinerea ssDNA virus 1 (BcssDV1), a tetrasegmented single-stranded DNA virus infecting the fungus Botrytis cinerea, has been molecularly characterized in this work. METHODS BcssDV1 was detected in Spanish and Italian B. cinerea field isolates obtained from grapevine. BcssDV1 variants genomes were molecularly characterized via NGS and Sanger sequencing. Nucleotide and amino acid sequences were used for diversity and phylogenetic analysis. Prediction of protein tertiary structures and putative associated functions were performed by AlphaFold2 and DALI. RESULTS BcssDV1 is a tetrasegmented single-stranded DNA virus. The mycovirus was composed by four genomic segments of approximately 1.7 Kb each, which are DNA-A, DNA-B, and DNA-C and DNA-D, that coded, respectively, for the rolling-circle replication initiation protein (Rep), capsid protein (CP) and two hypothetical proteins. BcssDV1 was present in several Italian and Spanish regions with high incidence and low variability among the different viral variants. DNA-A and DNA-D were found to be the more conserved genomic segments among variants, while DNA-B and DNA-C segments were shown to be the most variable ones. Tertiary structures of the proteins encoded by each segment suggested specific functions associated with each of them. CONCLUSIONS This study presented the first complete sequencing and characterization of a tetrasegmented ssDNA mycovirus, its incidence in Spain and Italy, its presence in other countries and its high conservation among regions.
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Affiliation(s)
- Ana Ruiz-Padilla
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (UPM-INIA/CSIC), Pozuelo de Alarcón, Madrid, Spain
| | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy, Torino, Italy
| | - María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (UPM-INIA/CSIC), Pozuelo de Alarcón, Madrid, Spain.
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain.
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Kundu S, Nunes L, Adler J, Mathot L, Stoimenov I, Sjöblom T. Recurring EPHB1 mutations in human cancers alter receptor signalling and compartmentalisation of colorectal cancer cells. Cell Commun Signal 2023; 21:354. [PMID: 38102712 PMCID: PMC10722860 DOI: 10.1186/s12964-023-01378-9] [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: 08/25/2023] [Accepted: 11/01/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Ephrin (EPH) receptors have been implicated in tumorigenesis and metastasis, but the functional understanding of mutations observed in human cancers is limited. We previously demonstrated reduced cell compartmentalisation for somatic EPHB1 mutations found in metastatic colorectal cancer cases. We therefore integrated pan-cancer and pan-EPH mutational data to prioritise recurrent EPHB1 mutations for functional studies to understand their contribution to cancer development and metastasis. METHODS Here, 79,151 somatic mutations in 9,898 samples of 33 different tumour types were analysed with a bioinformatic pipeline to find 3D-mutated cluster pairs and hotspot mutations in EPH receptors. From these, 15 recurring EPHB1 mutations were stably expressed in colorectal cancer followed by confocal microscopy based in vitro compartmentalisation assays and phospho-proteome analysis. RESULTS The 3D-protein structure-based bioinformatics analysis resulted in 63% EPHB1 mutants with compartmentalisation phenotypes vs 43% for hotspot mutations. Whereas the ligand-binding domain mutations C61Y, R90C, and R170W, the fibronectin domain mutation R351L, and the kinase domain mutation D762N displayed reduced to strongly compromised cell compartmentalisation, the kinase domain mutations R743W and G821R enhanced this phenotype. While mutants with reduced compartmentalisation also had reduced ligand induced receptor phosphorylation, the enhanced compartmentalisation was not linked to receptor phosphorylation level. Phosphoproteome mapping pinpointed the PI3K pathway and PIK3C2B phosphorylation in cells harbouring mutants with reduced compartmentalisation. CONCLUSIONS This is the first integrative study of pan-cancer EPH receptor mutations followed by in vitro validation, a robust way to identify cancer-causing mutations, uncovering EPHB1 mutation phenotypes and demonstrating the utility of protein structure-based mutation analysis in characterization of novel cancer genes. Video Abstract.
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Affiliation(s)
- Snehangshu Kundu
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Luís Nunes
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jeremy Adler
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lucy Mathot
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ivaylo Stoimenov
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tobias Sjöblom
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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Shi X, Lingerak R, Herting CJ, Ge Y, Kim S, Toth P, Wang W, Brown BP, Meiler J, Sossey-Alaoui K, Buck M, Himanen J, Hambardzumyan D, Nikolov DB, Smith AW, Wang B. Time-resolved live-cell spectroscopy reveals EphA2 multimeric assembly. Science 2023; 382:1042-1050. [PMID: 37972196 PMCID: PMC11114627 DOI: 10.1126/science.adg5314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
Ephrin type-A receptor 2 (EphA2) is a receptor tyrosine kinase that initiates both ligand-dependent tumor-suppressive and ligand-independent oncogenic signaling. We used time-resolved, live-cell fluorescence spectroscopy to show that the ligand-free EphA2 assembles into multimers driven by two types of intermolecular interactions in the ectodomain. The first type entails extended symmetric interactions required for ligand-induced receptor clustering and tumor-suppressive signaling that inhibits activity of the oncogenic extracellular signal-regulated kinase (ERK) and protein kinase B (AKT) protein kinases and suppresses cell migration. The second type is an asymmetric interaction between the amino terminus and the membrane proximal domain of the neighboring receptors, which supports oncogenic signaling and promotes migration in vitro and tumor invasiveness in vivo. Our results identify the molecular interactions that drive the formation of the EphA2 multimeric signaling clusters and reveal the pivotal role of EphA2 assembly in dictating its opposing functions in oncogenesis.
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Affiliation(s)
- Xiaojun Shi
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Cleveland, OH 44109, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Ryan Lingerak
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Cleveland, OH 44109, USA
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Cameron J. Herting
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Emory University, Atlanta, GA 30322, USA
| | - Yifan Ge
- Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Soyeon Kim
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Cleveland, OH 44109, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Paul Toth
- Department of Chemistry, University of Akron, Akron, OH 44325, USA
| | - Wei Wang
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Cleveland, OH 44109, USA
| | - Benjamin P. Brown
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Khalid Sossey-Alaoui
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Cleveland, OH 44109, USA
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - Juha Himanen
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dolores Hambardzumyan
- Departments Oncological Sciences and Neurosurgery, Tisch Cancer Institute, Icahn School of Medicine, Mount Sinai, New York, NY 10029, USA
| | - Dimitar B. Nikolov
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Adam W. Smith
- Department of Chemistry, University of Akron, Akron, OH 44325, USA
| | - Bingcheng Wang
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Cleveland, OH 44109, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
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McKenzie DM, Wirth D, Pogorelov TV, Hristova K. Utility of FRET in studies of membrane protein oligomerization: The concept of the effective dissociation constant. Biophys J 2023; 122:4113-4120. [PMID: 37735871 PMCID: PMC10598290 DOI: 10.1016/j.bpj.2023.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/07/2023] [Accepted: 09/18/2023] [Indexed: 09/23/2023] Open
Abstract
The activity of many membrane receptors is controlled through their lateral association into dimers or higher-order oligomers. Although Förster resonance energy transfer (FRET) measurements have been used extensively to characterize the stability of receptor dimers, the utility of FRET in studies of larger oligomers has been limited. Here we introduce an effective equilibrium dissociation constant that can be extracted from FRET measurements for EphA2, a receptor tyrosine kinase (RTK) known to form active oligomers of heterogeneous distributions in response to its ligand ephrinA1-Fc. The newly introduced effective equilibrium dissociation constant has a well-defined physical meaning and biological significance. It denotes the receptor concentration for which half of the receptors are monomeric and inactive, and the other half are associated into oligomers and are active, irrespective of the exact oligomer size. This work introduces a new dimension to the utility of FRET in studies of membrane receptor association and signaling in the plasma membrane.
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Affiliation(s)
- Daniel M McKenzie
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, Maryland
| | - Daniel Wirth
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, Maryland
| | - Taras V Pogorelov
- Department of Chemistry, Center for Biophysics and Quantitative Biology, School of Chemical Sciences, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, Maryland.
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10
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Strong TA, Esquivel J, Wang Q, Ledon PJ, Wang H, Gaidosh G, Tse D, Pelaez D. Activation of multiple Eph receptors on neuronal membranes correlates with the onset of optic neuropathy. EYE AND VISION (LONDON, ENGLAND) 2023; 10:42. [PMID: 37779186 PMCID: PMC10544557 DOI: 10.1186/s40662-023-00359-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/11/2023] [Indexed: 10/03/2023]
Abstract
BACKGROUND Optic neuropathy is a major cause of irreversible blindness, yet the molecular determinants that contribute to neuronal demise have not been fully elucidated. Several studies have identified 'ephrin signaling' as one of the most dysregulated pathways in the early pathophysiology of optic neuropathy with varied etiologies. Developmentally, gradients in ephrin signaling coordinate retinotopic mapping via repulsive modulation of cytoskeletal dynamics in neuronal membranes. Little is known about the role ephrin signaling plays in the post-natal visual system and its correlation with the onset of optic neuropathy. METHODS Postnatal mouse retinas were collected for mass spectrometry analysis for erythropoietin-producing human hepatocellular (Eph) receptors. Optic nerve crush (ONC) model was employed to induce optic neuropathy, and proteomic changes during the acute phase of neuropathic onset were analyzed. Confocal and super-resolution microscopy determined the cellular localization of activated Eph receptors after ONC injury. Eph receptor inhibitors assessed the neuroprotective effect of ephrin signaling modulation. RESULTS Mass spectrometry revealed expression of seven Eph receptors (EphA2, A4, A5, B1, B2, B3, and B6) in postnatal mouse retinal tissue. Immunoblotting analysis indicated a significant increase in phosphorylation of these Eph receptors 48 h after ONC. Confocal microscopy demonstrated the presence of both subclasses of Eph receptors within the retina. Stochastic optical reconstruction microscopy (STORM) super-resolution imaging combined with optimal transport colocalization analysis revealed a significant co-localization of activated Eph receptors with injured neuronal cells, compared to uninjured neuronal and/or injured glial cells, 48 h post-ONC. Eph receptor inhibitors displayed notable neuroprotective effects for retinal ganglion cells (RGCs) after six days of ONC injury. CONCLUSIONS Our findings demonstrate the functional presence of diverse Eph receptors in the postnatal mammalian retina, capable of modulating multiple biological processes. Pan-Eph receptor activation contributes to the onset of neuropathy in optic neuropathies, with preferential activation of Eph receptors on neuronal processes in the inner retina following optic nerve injury. Notably, Eph receptor activation precedes neuronal loss. We observed a neuroprotective effect on RGCs upon inhibiting Eph receptors. Our study highlights the importance of investigating this repulsive pathway in early optic neuropathies and provides a comprehensive characterization of the receptors present in the developed retina of mice, relevant to both homeostasis and disease processes.
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Affiliation(s)
- Thomas A Strong
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. Nasser Al-Rashid Orbital Vision Research Center, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Miami, FL, 33136, USA
- Department of Cell Biology, University of Miami Miller School of Medicine, Miami, USA
| | - Juan Esquivel
- Department of Physics, University of Florida College of Liberal Arts and Sciences, Gainesville, FL, USA
| | - Qikai Wang
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. Nasser Al-Rashid Orbital Vision Research Center, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Miami, FL, 33136, USA
| | - Paul J Ledon
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. Nasser Al-Rashid Orbital Vision Research Center, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Miami, FL, 33136, USA
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Hua Wang
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. Nasser Al-Rashid Orbital Vision Research Center, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Miami, FL, 33136, USA
| | - Gabriel Gaidosh
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - David Tse
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. Nasser Al-Rashid Orbital Vision Research Center, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Miami, FL, 33136, USA
| | - Daniel Pelaez
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, USA.
- Dr. Nasser Al-Rashid Orbital Vision Research Center, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Miami, FL, 33136, USA.
- Department of Biomedical Engineering, University of Miami College of Engineering, University of Miami, Coral Gables, FL, USA.
- Department of Cell Biology, University of Miami Miller School of Medicine, Miami, USA.
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA.
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11
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Stergiou IE, Papadakos SP, Karyda A, Tsitsilonis OE, Dimopoulos MA, Theocharis S. EPH/Ephrin Signaling in Normal Hematopoiesis and Hematologic Malignancies: Deciphering Their Intricate Role and Unraveling Possible New Therapeutic Targets. Cancers (Basel) 2023; 15:3963. [PMID: 37568780 PMCID: PMC10417178 DOI: 10.3390/cancers15153963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023] Open
Abstract
Erythropoietin-producing hepatocellular carcinoma receptors (EPHs) represent the largest family of receptor tyrosine kinases (RTKs). EPH interaction with ephrins, their membrane-bound ligands, holds a pivotal role in embryonic development, while, though less active, it is also implicated in various physiological functions during adult life. In normal hematopoiesis, different patterns of EPH/ephrin expression have been correlated with hematopoietic stem cell (HSC) maintenance and lineage-committed hematopoietic progenitor cell (HPC) differentiation, as well as with the functional properties of their mature offspring. Research in the field of hematologic malignancies has unveiled a rather complex involvement of the EPH/ephrinsignaling pathway in the pathophysiology of these neoplasms. Aberrations in genetic, epigenetic, and protein levels have been identified as possible players implicated both in tumor progression and suppression, while correlations have also been highlighted regarding prognosis and response to treatment. Initial efforts to therapeutically target the EPH/ephrin axis have been undertaken in the setting of hematologic neoplasia but are mainly confined to the preclinical level. To this end, deciphering the complexity of this signaling pathway both in normal and malignant hematopoiesis is necessary.
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Affiliation(s)
- Ioanna E. Stergiou
- Department of Pathophysiology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Stavros P. Papadakos
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.P.P.); (A.K.)
| | - Anna Karyda
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.P.P.); (A.K.)
| | - Ourania E. Tsitsilonis
- Flow Cytometry Unit, Department of Biology, School of Science, National and Kapodistrian University of Athens, 15784 Athens, Greece;
| | - Meletios-Athanasios Dimopoulos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Alexandra Hospital, 11528 Athens, Greece
| | - Stamatios Theocharis
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.P.P.); (A.K.)
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12
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Goncalves BG, Banerjee IA. A computational and laboratory approach for the investigation of interactions of peptide conjugated natural terpenes with EpHA2 receptor. J Mol Model 2023; 29:204. [PMID: 37291458 DOI: 10.1007/s00894-023-05596-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 05/17/2023] [Indexed: 06/10/2023]
Abstract
CONTEXT Ephrin type A receptor 2 (EphA2) is a well-known drug target for cancer treatment due to its overexpression in numerous types of cancers. Thus, it is crucial to determine the binding interactions of this receptor with both the ligand-binding domain (LBD) and the kinase-binding domain (KBD) through a targeted approach in order to modulate its activity. In this work, natural terpenes with inherent anticancer properties were conjugated with short peptides YSAYP and SWLAY that are known to bind to the LBD of EphA2 receptor. We examined the binding interactions of six terpenes (maslinic acid, levopimaric acid, quinopimaric acid, oleanolic, polyalthic, and hydroxybetulinic acid) conjugated to the above peptides with the ligand-binding domain (LBD) of EphA2 receptor computationally. Additionally, following the "target-hopping approach," we also examined the interactions of the conjugates with the KBD. Our results indicated that most of the conjugates showed higher binding interactions with the EphA2 kinase domain compared to LBD. Furthermore, the binding affinities of the terpenes increased upon conjugating the peptides with the terpenes. In order to further investigate the specificity toward EphA2 kinase domain, we also examined the binding interactions of the terpenes conjugated to VPWXE (x = norleucine), as VPWXE has been shown to bind to other RTKs. Our results indicated that the terpenes conjugated to SWLAY in particular showed high efficacy toward binding to the KBD. We also designed conjugates where in the peptide portion and the terpenes were separated by a butyl (C4) group linker to examine if the binding interactions could be enhanced. Docking studies showed that the conjugates with linkers had enhanced binding with the LBD compared to those without linkers, though binding remained slightly higher without linkers toward the KBD. As a proof of concept, maslinate and oleanolate conjugates of each of the peptides were then tested with F98 tumor cells which are known to overexpress EphA2 receptor. Results indicated that the oleanolate-amido-SWLAY conjugates were efficacious in reducing the cell proliferation of the tumor cells and may be potentially developed and further studied for targeting tumor cells overexpressing the EphA2 receptor. To test if these conjugates could bind to the receptor and potentially function as kinase inhibitors, we conducted SPR analysis and ADP-Glo assay. Our results indicated that OA conjugate with SWLAY showed the highest inhibition. METHODS Docking studies were carried out using AutoDock Vina, v.1.2.0; Molecular Dynamics and MMGBSA calculations were carried out through Schrodinger Software DESMOND.
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Affiliation(s)
- Beatriz G Goncalves
- Department of Chemistry, Fordham University, 441 East Fordham Road, Bronx, NY, 10458, USA
| | - Ipsita A Banerjee
- Department of Chemistry, Fordham University, 441 East Fordham Road, Bronx, NY, 10458, USA.
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13
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Strong TA, Esquivel J, Wang Q, Ledon PJ, Wang H, Gaidosh G, Tse D, Pelaez D. Activation of Multiple Eph Receptors on Neuronal Membranes Correlates with The Onset of Traumatic Optic Neuropathy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543735. [PMID: 37333178 PMCID: PMC10274644 DOI: 10.1101/2023.06.05.543735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Background Optic neuropathy (ON) is a major cause of irreversible blindness, yet the molecular determinants that contribute to neuronal demise have not been fully elucidated. Several studies have identified 'ephrin signaling' as one of the most dysregulated pathways in the early pathophysiology of ON with varied etiologies. Developmentally, gradients in ephrin signaling coordinate retinotopic mapping via repulsive modulation of cytoskeletal dynamics in neuronal membranes. Little is known about the role ephrin signaling played in the post-natal visual system and its correlation with the onset of optic neuropathy. Methods Postnatal mouse retinas were collected for mass spectrometry analysis for Eph receptors. Optic nerve crush (ONC) model was employed to induce optic neuropathy, and proteomic changes during the acute phase of neuropathic onset were analyzed. Confocal and super-resolution microscopy determined the cellular localization of activated Eph receptors after ONC injury. Eph receptor inhibitors assessed the neuroprotective effect of ephrin signaling modulation. Results Mass spectrometry revealed expression of seven Eph receptors (EphA2, A4, A5, B1, B2, B3, and B6) in postnatal mouse retinal tissue. Immunoblotting analysis indicated a significant increase in phosphorylation of these Eph receptors 48 hours after ONC. Confocal microscopy demonstrated the presence of both subclasses of Eph receptors in the inner retinal layers. STORM super-resolution imaging combined with optimal transport colocalization analysis revealed a significant co-localization of activated Eph receptors with injured neuronal processes, compared to uninjured neuronal and/or injured glial cells, 48 hours post-ONC. Eph receptor inhibitors displayed notable neuroprotective effects after 6 days of ONC injury. Conclusions Our findings demonstrate the functional presence of diverse Eph receptors in the postnatal mammalian retina, capable of modulating multiple biological processes. Pan-Eph receptor activation contributes to the onset of neuropathy in ONs, with preferential activation of Eph receptors on neuronal processes in the inner retina following optic nerve injury. Notably, Eph receptor activation precedes neuronal loss. We observed neuroprotective effects upon inhibiting Eph receptors. Our study highlights the importance of investigating this repulsive pathway in early optic neuropathies and provides a comprehensive characterization of the receptors present in the developed retina of mice, relevant to both homeostasis and disease processes.
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Affiliation(s)
- Thomas A. Strong
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, United States of America
- Dr. Nasser Al-Rashid Orbital Vision Research Center, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, United States of America
- Department of Cell Biology, University of Miami Miller School of Medicine
| | - Juan Esquivel
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, United States of America
| | - Qikai Wang
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, United States of America
- Dr. Nasser Al-Rashid Orbital Vision Research Center, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, United States of America
| | - Paul J. Ledon
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, United States of America
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, United States of America
| | - Hua Wang
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, United States of America
- Dr. Nasser Al-Rashid Orbital Vision Research Center, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, United States of America
| | - Gabriel Gaidosh
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, United States of America
| | - David Tse
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, United States of America
- Dr. Nasser Al-Rashid Orbital Vision Research Center, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, United States of America
| | - Daniel Pelaez
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, United States of America
- Dr. Nasser Al-Rashid Orbital Vision Research Center, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, United States of America
- Department of Biomedical Engineering, University of Miami College of Engineering, University of Miami, Coral Gables, FL, United States of America
- Department of Cell Biology, University of Miami Miller School of Medicine
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, United States of America
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14
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Waller V, Tschanz F, Winkler R, Pruschy M. The role of EphA2 in ADAM17- and ionizing radiation-enhanced lung cancer cell migration. Front Oncol 2023; 13:1117326. [PMID: 36998455 PMCID: PMC10043294 DOI: 10.3389/fonc.2023.1117326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/01/2023] [Indexed: 03/17/2023] Open
Abstract
PurposeIonizing radiation (IR) enhances the migratory capacity of cancer cells. Here we investigate in non-small-cell-lung-cancer (NSCLC) cells a novel link between IR-enhanced ADAM17 activity and the non-canonical pathway of EphA2 in the cellular stress response to irradiation.MethodsCancer cell migration in dependence of IR, EphA2, and paracrine signaling mediated by ADAM17 was determined using transwell migration assays. Changes of EphA2 pS897 and mRNA expression levels upon different ADAM17-directed treatment strategies, including the small molecular inhibitor TMI-005, the monoclonal antibody MEDI3622, and shRNAs, were mechanistically investigated. ADAM17-mediated release and cleavage of the EphA2 ligand ephrin-A1 was measured using ELISA and an acellular cleavage assay.ResultsIrradiation with 5 Gy enhanced tumor cell migration of NSCLC NCI-H358 cells in dependence of EphA2. At the same time, IR increased growth factor-induced EphA2 S897 phosphorylation via auto- and paracrine signaling. Genetic and pharmaceutical downregulation of ADAM17 activity abrogated growth factor (e.g. amphiregulin) release, which reduced MAPK pathway-mediated EphA2 S897 phosphorylation in an auto- and paracrine way (non-canonical EphA2-pathway) in NCI-H358 and A549 cells. These signaling processes were associated with reduced cell migration towards conditioned media derived from ADAM17-deficient cells. Interestingly, ADAM17 inhibition with the small molecular inhibitor TMI-005 led to the internalization and proteasomal degradation of EphA2, which was rescued by amphiregulin or MG-132 treatment. In addition, ADAM17 inhibition also abrogated ephrin-A1 cleavage and thereby interfered with the canonical EphA2-pathway.ConclusionWe identified ADAM17 and the receptor tyrosine kinase EphA2 as two important drivers for (IR-) induced NSCLC cell migration and described a unique interrelation between ADAM17 and EphA2. We demonstrated that ADAM17 influences both, EphA2 (pS897) and its GPI-anchored ligand ephrin-A1. Using different cellular and molecular readouts, we generated a comprehensive picture of how ADAM17 and IR influence the EphA2 canonical and non-canonical pathway in NSCLC cells.
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15
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Du G, Zhao L, Zheng Y, Belfetmi A, Cai T, Xu B, Heyninck K, Van Den Heede K, Buyse MA, Fontana P, Bowman M, Lin LL, Wu H, Chou JJ. Autoinhibitory structure of preligand association state implicates a new strategy to attain effective DR5 receptor activation. Cell Res 2023; 33:131-146. [PMID: 36604598 PMCID: PMC9892523 DOI: 10.1038/s41422-022-00755-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 11/15/2022] [Indexed: 01/07/2023] Open
Abstract
Members of the tumor necrosis factor receptor superfamily (TNFRSF) are important therapeutic targets that can be activated to induce death of cancer cells or stimulate proliferation of immune cells. Although it has long been implicated that these receptors assemble preligand associated states that are required for dominant interference in human disease, such states have so far eluded structural characterization. Here, we find that the ectodomain of death receptor 5 (DR5-ECD), a representative member of TNFRSF, can specifically self-associate when anchored to lipid bilayer, and we report this self-association structure determined by nuclear magnetic resonance (NMR). Unexpectedly, two non-overlapping interaction interfaces are identified that could propagate to higher-order clusters. Structure-guided mutagenesis indicates that the observed preligand association structure is represented on DR5-expressing cells. The DR5 preligand association serves an autoinhibitory role as single-domain antibodies (sdAbs) that partially dissociate the preligand cluster can sensitize the receptor to its ligand TRAIL and even induce substantial receptor signaling in the absence of TRAIL. Unlike most agonistic antibodies that require multivalent binding to aggregate receptors for activation, these agonistic sdAbs are monovalent and act specifically on an oligomeric, autoinhibitory configuration of the receptor. Our data indicate that receptors such as DR5 can form structurally defined preclusters incompatible with signaling and that true agonists should disrupt the preligand cluster while converting it to signaling-productive cluster. This mechanism enhances our understanding of a long-standing question in TNFRSF signaling and suggests a new opportunity for developing agonistic molecules by targeting receptor preligand clustering.
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Affiliation(s)
- Gang Du
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Linlin Zhao
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yumei Zheng
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Anissa Belfetmi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Tiantian Cai
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Boying Xu
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | | | | | | | - Pietro Fontana
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Michael Bowman
- Checkpoint Immunology, Immunology & Inflammation, Sanofi, Cambridge, MA, USA
| | - Lih-Ling Lin
- Checkpoint Immunology, Immunology & Inflammation, Sanofi, Cambridge, MA, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
| | - James Jeiwen Chou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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16
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Eph Receptors in Cancer. Biomedicines 2023; 11:biomedicines11020315. [PMID: 36830852 PMCID: PMC9953285 DOI: 10.3390/biomedicines11020315] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/13/2023] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
Eph receptor tyrosine kinases play critical functions during development, in the formation of tissue and organ borders, and the vascular and neural systems. Uniquely among tyrosine kinases, their activities are controlled by binding to membrane-bound ligands, called ephrins. Ephs and ephrins generally have a low expression in adults, functioning mainly in tissue homeostasis and plasticity, but are often overexpressed in cancers, where they are especially associated with undifferentiated or progenitor cells, and with tumour development, vasculature, and invasion. Mutations in Eph receptors also occur in various tumour types and are suspected to promote tumourigenesis. Ephs and ephrins have the capacity to operate as both tumour promoters and tumour suppressors, depending on the circumstances. They have been demonstrated to impact tumour cell proliferation, migration, and invasion in vitro, as well as tumour development, angiogenesis, and metastases in vivo, making them potential therapeutic targets. However, successful development of therapies will require detailed understanding of the opposing roles of Ephs in various cancers. In this review, we discuss the variations in Eph expression and functions in a variety of malignancies. We also describe the multiple strategies that are currently available to target them in tumours, including preclinical and clinical development.
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17
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Ganguly D, Thomas JA, Ali A, Kumar R. Mechanistic and therapeutic implications of EphA-4 receptor tyrosine kinase in the pathogenesis of Alzheimer's disease. Eur J Neurosci 2022; 56:5532-5546. [PMID: 34989046 DOI: 10.1111/ejn.15591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/14/2021] [Accepted: 12/28/2021] [Indexed: 12/14/2022]
Abstract
Erythropoietin-producing hepatoma (Eph) receptors belong to a family of tyrosine kinase receptors that plays a pivotal role in the development of the brain. Eph can be divided broadly into two groups, namely, EphA and EphB, comprising nine and five members, respectively. In recent years, the role of EphA-4 has become increasingly apparent in the onset of Alzheimer's disease (AD). Emerging evidence suggests that EphA-4 results in synaptic dysfunction, which in turn promotes the progression of AD. Moreover, pharmacological or genetic ablation of EphA-4 in the murine model of AD can alleviate the symptoms. The current review summarizes different pathways by which EphA-4 can influence pathogenesis. Since, majority of the studies had reported the protective effect of EphA-4 inhibition during AD, designing therapeutics based on decreasing its enzymatic activity might be necessary for introducing the novel interventions. Therefore, the review described peptide and nanobodies inhibitors of EphA-4 that exhibit the potential to modulate EphA-4 and could be used as lead molecules for the targeted therapy of AD.
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Affiliation(s)
- Devargya Ganguly
- Department of Biotechnology, GITAM Institute of Sciences, GITAM (Deemed to be) University, Vishakhapatnam, India
| | - Joshua Abby Thomas
- Department of Biotechnology, GITAM Institute of Sciences, GITAM (Deemed to be) University, Vishakhapatnam, India
| | - Abid Ali
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Rahul Kumar
- Department of Biotechnology, GITAM Institute of Sciences, GITAM (Deemed to be) University, Vishakhapatnam, India
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18
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Pospíšil J, Hrabovský M, Bohačiaková D, Hovádková Z, Jurásek M, Mlčoušková J, Paruch K, Nevolová Š, Damborsky J, Hampl A, Jaros J. Geometric Control of Cell Behavior by Biomolecule Nanodistribution. ACS Biomater Sci Eng 2022; 8:4789-4806. [PMID: 36202388 PMCID: PMC9667466 DOI: 10.1021/acsbiomaterials.2c00650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Many dynamic interactions within the cell microenvironment
modulate
cell behavior and cell fate. However, the pathways and mechanisms
behind cell–cell or cell–extracellular matrix interactions
remain understudied, as they occur at a nanoscale level. Recent progress
in nanotechnology allows for mimicking of the microenvironment at
nanoscale in vitro; electron-beam lithography (EBL)
is currently the most promising technique. Although this nanopatterning
technique can generate nanostructures of good quality and resolution,
it has resulted, thus far, in the production of only simple shapes
(e.g., rectangles) over a relatively small area (100 × 100 μm),
leaving its potential in biological applications unfulfilled. Here,
we used EBL for cell-interaction studies by coating cell-culture-relevant
material with electron-conductive indium tin oxide, which formed nanopatterns
of complex nanohexagonal structures over a large area (500 ×
500 μm). We confirmed the potential of EBL for use in cell-interaction
studies by analyzing specific cell responses toward differentially
distributed nanohexagons spaced at 1000, 500, and 250 nm. We found
that our optimized technique of EBL with HaloTags enabled the investigation
of broad changes to a cell-culture-relevant surface and can provide
an understanding of cellular signaling mechanisms at a single-molecule
level.
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Affiliation(s)
- Jakub Pospíšil
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.,Core Facility Cellular Imaging, CEITEC, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Miloš Hrabovský
- TESCAN Orsay Holding a.s., Libušina tř. 863, Brno 623 00, Czech Republic
| | - Dáša Bohačiaková
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.,International Clinical Research Center (ICRC), St. Anne's University Hospital, Pekařská 53, Brno 656 91, Czech Republic
| | | | | | - Jarmila Mlčoušková
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Kamil Paruch
- International Clinical Research Center (ICRC), St. Anne's University Hospital, Pekařská 53, Brno 656 91, Czech Republic.,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Šárka Nevolová
- International Clinical Research Center (ICRC), St. Anne's University Hospital, Pekařská 53, Brno 656 91, Czech Republic.,Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Jiri Damborsky
- International Clinical Research Center (ICRC), St. Anne's University Hospital, Pekařská 53, Brno 656 91, Czech Republic.,Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Aleš Hampl
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.,International Clinical Research Center (ICRC), St. Anne's University Hospital, Pekařská 53, Brno 656 91, Czech Republic
| | - Josef Jaros
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.,International Clinical Research Center (ICRC), St. Anne's University Hospital, Pekařská 53, Brno 656 91, Czech Republic
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19
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Zapata-Mercado E, Biener G, McKenzie DM, Wimley WC, Pasquale EB, Raicu V, Hristova K. The efficacy of receptor tyrosine kinase EphA2 autophosphorylation increases with EphA2 oligomer size. J Biol Chem 2022; 298:102370. [PMID: 35970390 PMCID: PMC9512837 DOI: 10.1016/j.jbc.2022.102370] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/30/2022] Open
Abstract
The receptor tyrosine kinase (RTK) EphA2 is expressed in epithelial and endothelial cells and controls the assembly of cell-cell junctions. EphA2 has also been implicated in many diseases, including cancer. Unlike most RTKs, which signal predominantly as dimers, EphA2 readily forms high-order oligomers upon ligand binding. Here, we investigated if a correlation exists between EphA2 signaling properties and the size of the EphA2 oligomers induced by multiple ligands, including the widely used ephrinA1-Fc ligand, the soluble monomeric m-ephrinA1, and novel engineered peptide ligands. We used fluorescence intensity fluctuation (FIF) spectrometry to characterize the EphA2 oligomer populations induced by the different ligands. Interestingly, we found that different monomeric and dimeric ligands induce EphA2 oligomers with widely different size distributions. Our comparison of FIF brightness distribution parameters and EphA2 signaling parameters reveals that the efficacy of EphA2 phosphorylation on tyrosine 588, an autophosphorylation response contributing to EphA2 activation, correlates with EphA2 mean oligomer size. However, we found that other characteristics, such as the efficacy of AKT inhibition and ligand bias coefficients, appear to be independent of EphA2 oligomer size. Taken together, this work highlights the utility of FIF in RTK signaling research and demonstrates a quantitative correlation between the architecture of EphA2 signaling complexes and signaling features.
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Affiliation(s)
- Elmer Zapata-Mercado
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Gabriel Biener
- Department of Physics, University of Wisconsin, Milwaukee, Wisconsin, USA
| | - Daniel M McKenzie
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - William C Wimley
- Tulane University School of Medicine, Department of Biochemistry and Molecular Biology, New Orleans, Louisiana, USA
| | - Elena B Pasquale
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA.
| | - Valerica Raicu
- Department of Physics, University of Wisconsin, Milwaukee, Wisconsin, USA; Department of Biological Sciences, University of Wisconsin, Milwaukee, Wisconsin, USA.
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland, USA.
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20
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Abstract
Single-pass transmembrane receptors (SPTMRs) represent a diverse group of integral membrane proteins that are involved in many essential cellular processes, including signal transduction, cell adhesion, and transmembrane transport of materials. Dysregulation of the SPTMRs is linked with many human diseases. Despite extensive efforts in past decades, the mechanisms of action of the SPTMRs remain incompletely understood. One major hurdle is the lack of structures of the full-length SPTMRs in different functional states. Such structural information is difficult to obtain by traditional structural biology methods such as X-ray crystallography and nuclear magnetic resonance (NMR). The recent rapid development of single-particle cryo-electron microscopy (cryo-EM) has led to an exponential surge in the number of high-resolution structures of integral membrane proteins, including SPTMRs. Cryo-EM structures of SPTMRs solved in the past few years have tremendously improved our understanding of how SPTMRs function. In this review, we will highlight these progresses in the structural studies of SPTMRs by single-particle cryo-EM, analyze important structural details of each protein involved, and discuss their implications on the underlying mechanisms. Finally, we also briefly discuss remaining challenges and exciting opportunities in the field.
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Affiliation(s)
- Kai Cai
- Departments of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
| | - Xuewu Zhang
- Departments of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Departments of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Corresponding Author: Xuewu Zhang, Department of pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA;
| | - Xiao-chen Bai
- Departments of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Departments of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Corresponding Author: Xiao-chen Bai, Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390, USA;
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21
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Fan T, Liang B, Nie L, Wang J, Zhang H, Ciechanover A, Xu Y, An J, Huang Z. A synthetic bivalent peptide ligand of EphB4 with potent agonistic activity. Eur J Med Chem 2022; 244:114804. [DOI: 10.1016/j.ejmech.2022.114804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/21/2022] [Accepted: 09/26/2022] [Indexed: 12/01/2022]
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22
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Unexpected structures formed by the kinase RET C634R mutant extracellular domain suggest potential oncogenic mechanisms in MEN2A. J Biol Chem 2022; 298:102380. [PMID: 35985422 PMCID: PMC9490035 DOI: 10.1016/j.jbc.2022.102380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 07/31/2022] [Accepted: 08/03/2022] [Indexed: 11/25/2022] Open
Abstract
The RET receptor tyrosine kinase plays a pivotal role in cell survival, proliferation, and differentiation, and its abnormal activation leads to cancers through receptor fusions or point mutations. Mutations that disrupt the disulfide network in the extracellular domain (ECD) of RET drive multiple endocrine neoplasia type 2A (MEN2A), a hereditary syndrome associated with the development of thyroid cancers. However, structural details of how specific mutations affect RET are unclear. Here, we present the first structural insights into the ECD of the RET(C634R) mutant, the most common mutation in MEN2A. Using electron microscopy, we demonstrate that the C634R mutation causes ligand-independent dimerization of the RET ECD, revealing an unusual tail-to-tail conformation that is distinct from the ligand-induced signaling dimer of WT RET. Additionally, we show that the RETC634R ECD dimer can form complexes with at least two of the canonical RET ligands and that these complexes form very different structures than WT RET ECD upon ligand binding. In conclusion, this structural analysis of cysteine-mutant RET ECD suggests a potential key mechanism of cancer induction in MEN2A, both in the absence and presence of its native ligands, and may offer new targets for therapeutic intervention.
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23
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Oh D, Chen Z, Biswas KH, Bai F, Ong HT, Sheetz MP, Groves JT. Competition for shared downstream signaling molecules establishes indirect negative feedback between EGFR and EphA2. Biophys J 2022; 121:1897-1908. [DOI: 10.1016/j.bpj.2022.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/21/2022] [Accepted: 04/12/2022] [Indexed: 11/02/2022] Open
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24
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Gomez-Soler M, Gehring MP, Lechtenberg BC, Zapata-Mercado E, Ruelos A, Matsumoto MW, Hristova K, Pasquale EB. Ligands with different dimeric configurations potently activate the EphA2 receptor and reveal its potential for biased signaling. iScience 2022; 25:103870. [PMID: 35243233 PMCID: PMC8858996 DOI: 10.1016/j.isci.2022.103870] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/13/2021] [Accepted: 02/01/2022] [Indexed: 12/03/2022] Open
Abstract
The EphA2 receptor tyrosine kinase activates signaling pathways with different, and sometimes opposite, effects in cancer and other pathologies. Thus, highly specific and potent biased ligands that differentially control EphA2 signaling responses could be therapeutically valuable. Here, we use EphA2-specific monomeric peptides to engineer dimeric ligands with three different geometric configurations to combine a potential ability to differentially modulate EphA2 signaling responses with the high potency and prolonged receptor residence time characteristic of dimeric ligands. The different dimeric peptides readily induce EphA2 clustering, autophosphorylation and signaling, the best with sub-nanomolar potency. Yet, there are differences in two EphA2 signaling responses induced by peptides with different configurations, which exhibit distinct potency and efficacy. The peptides bias signaling when compared with the ephrinA1-Fc ligand and do so via different mechanisms. These findings provide insights into Eph receptor signaling, and proof-of-principle that different Eph signaling responses can be distinctly modulated.
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Affiliation(s)
- Maricel Gomez-Soler
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Marina P. Gehring
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Bernhard C. Lechtenberg
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville Victoria 3052, Australia and Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Elmer Zapata-Mercado
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alyssa Ruelos
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Mike W. Matsumoto
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Elena B. Pasquale
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
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25
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Abstract
The EPH receptor tyrosine kinases and their signaling partners, the EPHRINS, comprise a large class of cell signaling molecules that plays diverse roles in development. As cell membrane-anchored signaling molecules, they regulate cellular organization by modulating the strength of cellular contacts, usually by impacting the actin cytoskeleton or cell adhesion programs. Through these cellular functions, EPH/EPHRIN signaling often regulates tissue shape. Indeed, recent evidence indicates that this signaling family is ancient and associated with the origin of multicellularity. Though extensively studied, our understanding of the signaling mechanisms employed by this large family of signaling proteins remains patchwork, and a truly "canonical" EPH/EPHRIN signal transduction pathway is not known and may not exist. Instead, several foundational evolutionarily conserved mechanisms are overlaid by a myriad of tissue -specific functions, though common themes emerge from these as well. Here, I review recent advances and the related contexts that have provided new understanding of the conserved and varied molecular and cellular mechanisms employed by EPH/EPHRIN signaling during development.
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Affiliation(s)
- Jeffrey O Bush
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, United States; Program in Craniofacial Biology, University of California San Francisco, San Francisco, CA, United States; Institute for Human Genetics, University of California San Francisco, San Francisco, CA, United States; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, United States.
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26
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Regulation of the EphA2 receptor intracellular region by phosphomimetic negative charges in the kinase-SAM linker. Nat Commun 2021; 12:7047. [PMID: 34857764 PMCID: PMC8639986 DOI: 10.1038/s41467-021-27343-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 11/11/2021] [Indexed: 11/22/2022] Open
Abstract
Eph receptor tyrosine kinases play a key role in cell-cell communication. Lack of structural information on the entire multi-domain intracellular region of any Eph receptor has hindered understanding of their signaling mechanisms. Here, we use integrative structural biology to investigate the structure and dynamics of the EphA2 intracellular region. EphA2 promotes cancer malignancy through a poorly understood non-canonical form of signaling involving serine/threonine phosphorylation of the linker connecting its kinase and SAM domains. We show that accumulation of multiple linker negative charges, mimicking phosphorylation, induces cooperative changes in the EphA2 intracellular region from more closed to more extended conformations and perturbs the EphA2 juxtamembrane segment and kinase domain. In cells, linker negative charges promote EphA2 oligomerization. We also identify multiple kinases catalyzing linker phosphorylation. Our findings suggest multiple effects of linker phosphorylation on EphA2 signaling and imply that coordination of different kinases is necessary to promote EphA2 non-canonical signaling. Eph receptor tyrosine kinases and their ephrin ligands mediate cell-cell communication. Here, the authors assess the structure and dynamics of the EphA2 intracellular region and uncover complex effects of phosphorylation within the linker region between EphA2 kinase and SAM domains.
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27
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Nilvebrant J, Ereño-Orbea J, Gorelik M, Julian MC, Tessier PM, Julien JP, Sidhu SS. Systematic Engineering of Optimized Autonomous Heavy-Chain Variable Domains. J Mol Biol 2021; 433:167241. [PMID: 34508727 DOI: 10.1016/j.jmb.2021.167241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/16/2021] [Accepted: 09/03/2021] [Indexed: 01/06/2023]
Abstract
Autonomous heavy-chain variable (VH) domains are the smallest functional antibody fragments, and they possess unique features, including small size and convex paratopes, which provide enhanced targeting of concave epitopes that are difficult to access with larger conventional antibodies. However, human VH domains have evolved to fold and function with a light chain partner, and alone, they typically suffer from low stability and high aggregation propensity. Development of autonomous human VH domains, in which aggregation propensity is reduced without compromising antigen recognition, has proven challenging. Here, we used an autonomous human VH domain as a scaffold to construct phage-displayed synthetic libraries in which aspartate was systematically incorporated at different paratope positions. In selections, the library yielded many anti-EphA1 receptor VH domains, which were characterized in detail. Structural analyses of a parental anti-EphA1 VH domain and an improved variant provided insights into the effects of aspartate and other substitutions on preventing aggregation while retaining function. Our naïve libraries and in vitro selection procedures offer a systematic approach to generating highly functional autonomous human VH domains that resist aggregation and could be used for basic research and biomedical applications.
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Affiliation(s)
- Johan Nilvebrant
- Banting and Best Department of Medical Research and Department of Molecular Genetics, The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - June Ereño-Orbea
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute and Departments of Biochemistry and Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Maryna Gorelik
- Banting and Best Department of Medical Research and Department of Molecular Genetics, The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Mark C Julian
- Isermann Department of Chemical & Biological Engineering, Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Peter M Tessier
- Isermann Department of Chemical & Biological Engineering, Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Departments of Chemical Engineering, Pharmaceutical Sciences, and Biomedical Engineering, Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute and Departments of Biochemistry and Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Sachdev S Sidhu
- Banting and Best Department of Medical Research and Department of Molecular Genetics, The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada.
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28
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Xu Y, Robev D, Saha N, Wang B, Dalva MB, Xu K, Himanen JP, Nikolov DB. The Ephb2 Receptor Uses Homotypic, Head-to-Tail Interactions within Its Ectodomain as an Autoinhibitory Control Mechanism. Int J Mol Sci 2021; 22:10473. [PMID: 34638814 PMCID: PMC8508685 DOI: 10.3390/ijms221910473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022] Open
Abstract
The Eph receptor tyrosine kinases and their ephrin ligands direct axon pathfinding and neuronal cell migration, as well as mediate many other cell-cell communication events. Their dysfunctional signaling has been shown to lead to various diseases, including cancer. The Ephs and ephrins both localize to the plasma membrane and, upon cell-cell contact, form extensive signaling assemblies at the contact sites. The Ephs and the ephrins are divided into A and B subclasses based on their sequence conservation and affinities for each other. The molecular details of Eph-ephrin recognition have been previously revealed and it has been documented that ephrin binding induces higher-order Eph assemblies, which are essential for full biological activity, via multiple, distinct Eph-Eph interfaces. One Eph-Eph interface type is characterized by a homotypic, head-to-tail interaction between the ligand-binding and the fibronectin domains of two adjacent Eph molecules. While the previous Eph ectodomain structural studies were focused on A class receptors, we now report the crystal structure of the full ectodomain of EphB2, revealing distinct and unique head-to-tail receptor-receptor interactions. The EphB2 structure and structure-based mutagenesis document that EphB2 uses the head-to-tail interactions as a novel autoinhibitory control mechanism for regulating downstream signaling and that these interactions can be modulated by posttranslational modifications.
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Affiliation(s)
- Yan Xu
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA; (Y.X.); (K.X.)
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; (D.R.); (N.S.)
| | - Dorothea Robev
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; (D.R.); (N.S.)
| | - Nayanendu Saha
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; (D.R.); (N.S.)
| | - Bingcheng Wang
- Rammelkamp Center for Research, MetroHealth Medical Center, 2500 MetroHealth Drive, Cleveland, OH 44109, USA;
| | - Matthew B. Dalva
- Department of Neuroscience and Jefferson Center for Synaptic Biology, Thomas Jefferson University, 233 South 10th Street, Bluemle Life Sciences Building, Room 324, Philadelphia, PA 19107, USA;
| | - Kai Xu
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA; (Y.X.); (K.X.)
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; (D.R.); (N.S.)
| | - Juha P. Himanen
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; (D.R.); (N.S.)
| | - Dimitar B. Nikolov
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; (D.R.); (N.S.)
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29
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Dynamic Effects in Nucleation of Receptor Clusters. ENTROPY 2021; 23:e23101245. [PMID: 34681969 PMCID: PMC8534492 DOI: 10.3390/e23101245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022]
Abstract
Nucleation theory has been widely applied for the interpretation of critical phenomena in nonequilibrium systems. Ligand-induced receptor clustering is a critical step of cellular activation. Receptor clusters on the cell surface are treated from the nucleation theory point of view. The authors propose that the redistribution of energy over the degrees of freedom is crucial for forming each new bond in the growing cluster. The expression for a kinetic barrier for new bond formation in a cluster was obtained. The shape of critical receptor clusters seems to be very important for the clustering on the cell surface. The von Neumann entropy of the graph of bonds is used to determine the influence of the cluster shape on the kinetic barrier. Numerical studies were carried out to assess the dependence of the barrier on the size of the cluster. The asymptotic expression, reflecting the conditions necessary for the formation of receptor clusters, was obtained. Several dynamic effects were found. A slight increase of the ligand mass has been shown to significantly accelerate the nucleation of receptor clusters. The possible meaning of the obtained results for medical applications is discussed.
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30
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Liang LY, Roy M, Horne CR, Sandow JJ, Surudoi M, Dagley LF, Young SN, Dite T, Babon JJ, Janes PW, Patel O, Murphy JM, Lucet IS. The intracellular domains of the EphB6 and EphA10 receptor tyrosine pseudokinases function as dynamic signalling hubs. Biochem J 2021; 478:3351-3371. [PMID: 34431498 PMCID: PMC8454701 DOI: 10.1042/bcj20210572] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 12/25/2022]
Abstract
EphB6 and EphA10 are two poorly characterised pseudokinase members of the Eph receptor family, which collectively serves as mediators of contact-dependent cell-cell communication to transmit extracellular cues into intracellular signals. As per their active counterparts, EphB6 and EphA10 deregulation is strongly linked to proliferative diseases. However, unlike active Eph receptors, whose catalytic activities are thought to initiate an intracellular signalling cascade, EphB6 and EphA10 are classified as catalytically dead, raising the question of how non-catalytic functions contribute to Eph receptor signalling homeostasis. In this study, we have characterised the biochemical properties and topology of the EphB6 and EphA10 intracellular regions comprising the juxtamembrane (JM) region, pseudokinase and SAM domains. Using small-angle X-ray scattering and cross-linking-mass spectrometry, we observed high flexibility within their intracellular regions in solution and a propensity for interaction between the component domains. We identified tyrosine residues in the JM region of EphB6 as EphB4 substrates, which can bind the SH2 domains of signalling effectors, including Abl, Src and Vav3, consistent with cellular roles in recruiting these proteins for downstream signalling. Furthermore, our finding that EphB6 and EphA10 can bind ATP and ATP-competitive small molecules raises the prospect that these pseudokinase domains could be pharmacologically targeted to counter oncogenic signalling.
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Affiliation(s)
- Lung-Yu Liang
- Walter and Eliza Hall Institute or Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Michael Roy
- Walter and Eliza Hall Institute or Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Christopher R. Horne
- Walter and Eliza Hall Institute or Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Jarrod J. Sandow
- Walter and Eliza Hall Institute or Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Minglyanna Surudoi
- Walter and Eliza Hall Institute or Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Laura F. Dagley
- Walter and Eliza Hall Institute or Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Samuel N. Young
- Walter and Eliza Hall Institute or Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Toby Dite
- Walter and Eliza Hall Institute or Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Jeffrey J. Babon
- Walter and Eliza Hall Institute or Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Peter W. Janes
- Tumour Targeting Program, Olivia Newton-John Cancer Research Institute and La Trobe School of Cancer Medicine, Level 5, ONJ Centre, 145 Studley Rd, Heidelberg, Victoria 3084, Australia
| | - Onisha Patel
- Walter and Eliza Hall Institute or Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - James M. Murphy
- Walter and Eliza Hall Institute or Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Isabelle S. Lucet
- Walter and Eliza Hall Institute or Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, Australia
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31
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Light TP, Brun D, Guardado-Calvo P, Pederzoli R, Haouz A, Neipel F, Rey FA, Hristova K, Backovic M. Human herpesvirus 8 molecular mimicry of ephrin ligands facilitates cell entry and triggers EphA2 signaling. PLoS Biol 2021; 19:e3001392. [PMID: 34499637 PMCID: PMC8454987 DOI: 10.1371/journal.pbio.3001392] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 09/21/2021] [Accepted: 08/16/2021] [Indexed: 01/19/2023] Open
Abstract
Human herpesvirus 8 (HHV-8) is an oncogenic virus that enters cells by fusion of the viral and endosomal cellular membranes in a process mediated by viral surface glycoproteins. One of the cellular receptors hijacked by HHV-8 to gain access to cells is the EphA2 tyrosine kinase receptor, and the mechanistic basis of EphA2-mediated viral entry remains unclear. Using X-ray structure analysis, targeted mutagenesis, and binding studies, we here show that the HHV-8 envelope glycoprotein complex H and L (gH/gL) binds with subnanomolar affinity to EphA2 via molecular mimicry of the receptor’s cellular ligands, ephrins (Eph family receptor interacting proteins), revealing a pivotal role for the conserved gH residue E52 and the amino-terminal peptide of gL. Using FSI-FRET and cell contraction assays, we further demonstrate that the gH/gL complex also functionally mimics ephrin ligand by inducing EphA2 receptor association via its dimerization interface, thus triggering receptor signaling for cytoskeleton remodeling. These results now provide novel insight into the entry mechanism of HHV-8, opening avenues for the search of therapeutic agents that could interfere with HHV-8–related diseases. Herpesviruses are known to hijack cellular receptors to enter cells, but this study shows that human herpesvirus 8 takes this to another level by using its envelope glycoprotein complex gH/gL to mimic the EphA2 receptor’s natural ligands, ephrins.
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Affiliation(s)
- Taylor P Light
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America.,Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Delphine Brun
- Department of Virology, Structural Virology Unit, Institut Pasteur, Paris, France.,CNRS, UMR 3569, Paris, France
| | - Pablo Guardado-Calvo
- Department of Virology, Structural Virology Unit, Institut Pasteur, Paris, France.,CNRS, UMR 3569, Paris, France
| | - Riccardo Pederzoli
- Department of Virology, Structural Virology Unit, Institut Pasteur, Paris, France.,CNRS, UMR 3569, Paris, France
| | - Ahmed Haouz
- CNRS, UMR 3569, Paris, France.,Crystallography Platform C2RT, Institut Pasteur, Paris, France
| | - Frank Neipel
- Crystallography Platform C2RT, Institut Pasteur, Paris, France
| | - Félix A Rey
- Department of Virology, Structural Virology Unit, Institut Pasteur, Paris, France.,CNRS, UMR 3569, Paris, France
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America.,Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Marija Backovic
- Department of Virology, Structural Virology Unit, Institut Pasteur, Paris, France.,CNRS, UMR 3569, Paris, France
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32
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Sahoo AR, Buck M. Structural and Functional Insights into the Transmembrane Domain Association of Eph Receptors. Int J Mol Sci 2021; 22:ijms22168593. [PMID: 34445298 PMCID: PMC8395321 DOI: 10.3390/ijms22168593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 12/04/2022] Open
Abstract
Eph receptors are the largest family of receptor tyrosine kinases and by interactions with ephrin ligands mediate a myriad of processes from embryonic development to adult tissue homeostasis. The interaction of Eph receptors, especially at their transmembrane (TM) domains is key to understanding their mechanism of signal transduction across cellular membranes. We review the structural and functional aspects of EphA1/A2 association and the techniques used to investigate their TM domains: NMR, molecular modelling/dynamics simulations and fluorescence. We also introduce transmembrane peptides, which can be used to alter Eph receptor signaling and we provide a perspective for future studies.
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Affiliation(s)
- Amita R. Sahoo
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA;
| | - Matthias Buck
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA;
- Department of Neurosciences, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Correspondence:
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33
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The EphB6 Receptor: Kinase-Dead but Very Much Alive. Int J Mol Sci 2021; 22:ijms22158211. [PMID: 34360976 PMCID: PMC8347583 DOI: 10.3390/ijms22158211] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 01/15/2023] Open
Abstract
The Eph receptor tyrosine kinase member EphB6 is a pseudokinase, and similar to other pseudoenzymes has not attracted an equivalent amount of interest as its enzymatically-active counterparts. However, a greater appreciation for the role pseudoenzymes perform in expanding the repertoire of signals generated by signal transduction systems has fostered more interest in the field. EphB6 acts as a molecular switch that is capable of modulating the signal transduction output of Eph receptor clusters. Although the biological effects of EphB6 activity are well defined, the molecular mechanisms of EphB6 function remain enigmatic. In this review, we use a comparative approach to postulate how EphB6 acts as a scaffold to recruit adaptor proteins to an Eph receptor cluster and how this function is regulated. We suggest that the evolutionary repurposing of EphB6 into a kinase-independent molecular switch in mammals has involved repurposing the kinase activation loop into an SH3 domain-binding site. In addition, we suggest that EphB6 employs the same SAM domain linker and juxtamembrane domain allosteric regulatory mechanisms that are used in kinase-positive Eph receptors to regulate its scaffold function. As a result, although kinase-dead, EphB6 remains a strategically active component of Eph receptor signaling.
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Westerfield JM, Sahoo AR, Alves DS, Grau B, Cameron A, Maxwell M, Schuster JA, Souza PCT, Mingarro I, Buck M, Barrera FN. Conformational Clamping by a Membrane Ligand Activates the EphA2 Receptor. J Mol Biol 2021; 433:167144. [PMID: 34229012 DOI: 10.1016/j.jmb.2021.167144] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/03/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023]
Abstract
The EphA2 receptor is a promising drug target for cancer treatment, since EphA2 activation can inhibit metastasis and tumor progression. It has been recently described that the TYPE7 peptide activates EphA2 using a novel mechanism that involves binding to the single transmembrane domain of the receptor. TYPE7 is a conditional transmembrane (TM) ligand, which only inserts into membranes at neutral pH in the presence of the TM region of EphA2. However, how membrane interactions can activate EphA2 is not known. We systematically altered the sequence of TYPE7 to identify the binding motif used to activate EphA2. With the resulting six peptides, we performed biophysical and cell migration assays that identified a new potent peptide variant. We also performed a mutational screen that determined the helical interface that mediates dimerization of the TM domain of EphA2 in cells. These results, together with molecular dynamic simulations, allowed to elucidate the molecular mechanism that TYPE7 uses to activate EphA2, where the membrane peptide acts as a molecular clamp that wraps around the TM dimer of the receptor. We propose that this binding mode stabilizes the active conformation of EphA2. Our data, additionally, provide clues into the properties that TM ligands need to have in order to achieve activation of membrane receptors.
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Affiliation(s)
- Justin M Westerfield
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Amita R Sahoo
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Daiane S Alves
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Brayan Grau
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Alayna Cameron
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Mikayla Maxwell
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Jennifer A Schuster
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS & University of Lyon, 7 Passage du Vercors, F-69367 Lyon, France
| | - Ismael Mingarro
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA.
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Enderle L, Shalaby KH, Gorelik M, Weiss A, Blazer LL, Paduch M, Cardarelli L, Kossiakoff A, Adams JJ, Sidhu SS. A T cell redirection platform for co-targeting dual antigens on solid tumors. MAbs 2021; 13:1933690. [PMID: 34190031 PMCID: PMC8253144 DOI: 10.1080/19420862.2021.1933690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
In order to direct T cells to specific features of solid cancer cells, we engineered a bispecific antibody format, named Dual Antigen T cell Engager (DATE), by fusing a single-chain variable fragment targeting CD3 to a tumor-targeting antigen-binding fragment. In this format, multiple novel paratopes against different tumor antigens were able to recruit T-cell cytotoxicity to tumor cells in vitro and in an in vivo pancreatic ductal adenocarcinoma xenograft model. Since unique surface antigens in solid tumors are limited, in order to enhance selectivity, we further engineered “double-DATEs” targeting two tumor antigens simultaneously. The double-DATE contains an additional autonomous variable heavy-chain domain, which binds a second tumor antigen without itself eliciting a cytotoxic response. This novel modality provides a strategy to enhance the selectivity of immune redirection through binary targeting of native tumor antigens. The modularity and use of a common, stable human framework for all components enables a pipeline approach to rapidly develop a broad repertoire of tailored DATEs and double-DATEs with favorable biophysical properties and high potencies and selectivities.
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Affiliation(s)
- Leonie Enderle
- Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Karim H Shalaby
- Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Maryna Gorelik
- Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Alexander Weiss
- Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Levi L Blazer
- Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Marcin Paduch
- Institute for Biophysical Dynamics, Gordon Center for Integrative Science, Chicago, USA
| | - Lia Cardarelli
- Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Anthony Kossiakoff
- Institute for Biophysical Dynamics, Gordon Center for Integrative Science, Chicago, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, USA
| | - Jarrett J Adams
- Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Sachdev S Sidhu
- Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
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Mason EO, Goldgur Y, Robev D, Freywald A, Nikolov DB, Himanen JP. Structure of the EphB6 receptor ectodomain. PLoS One 2021; 16:e0247335. [PMID: 33770085 PMCID: PMC7997048 DOI: 10.1371/journal.pone.0247335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/04/2021] [Indexed: 12/15/2022] Open
Abstract
Eph receptors are the largest group amongst the receptor tyrosine kinases and are divided into two subgroups, A and B, based on ligand binding specificities and sequence conservation. Through ligand-induced and ligand-independent activities, Ephs play central roles in diverse biological processes, including embryo development, regulation of neuronal signaling, immune responses, vasculogenesis, as well as tumor initiation, progression, and metastasis. The Eph extracellular regions (ECDs) are constituted of multiple domains, and previous structural studies of the A class receptors revealed how they interact with ephrin ligands and simultaneously mediate Eph-Eph clustering necessary for biological activity. Specifically, EphA structures highlighted a model, where clustering of ligand-bound receptors relies on two distinct receptor/receptor interfaces. Interestingly, most unliganded A class receptors also form an additional, third interface, between the ligand binding domain (LBD) and the fibronectin III domain (FN3) of neighboring molecules. Structures of B-class Eph ECDs, on the other hand, have never been reported. To further our understanding of Eph receptor function, we crystallized the EphB6-ECD and determined its three-dimensional structure using X-ray crystallography. EphB6 has important functions in both normal physiology and human malignancies and is especially interesting because this atypical receptor innately lacks kinase activity and our understanding of the mechanism of action is still incomplete. Our structural data reveals the overall EphB6-ECD architecture and shows EphB6-LBD/FN3 interactions similar to those observed for the unliganded A class receptors, suggesting that these unusual interactions are of general importance to the Eph group. We also observe unique structural features, which likely reflect the atypical signaling properties of EphB6, namely the need of co-receptor(s) for this kinase-inactive Eph. These findings provide new valuable information on the structural organization and mechanism of action of the B-class Ephs, and specifically EphB6, which in the future will assist in identifying clinically relevant targets for cancer therapy.
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Affiliation(s)
- Emilia O. Mason
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Yehuda Goldgur
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Dorothea Robev
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Dimitar B. Nikolov
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- * E-mail: (DBN); (JPH)
| | - Juha P. Himanen
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- * E-mail: (DBN); (JPH)
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Wang H, Hou W, Perera A, Bettler C, Beach JR, Ding X, Li J, Denning MF, Dhanarajan A, Cotler SJ, Joyce C, Yin J, Ahmed F, Roberts LR, Qiu W. Targeting EphA2 suppresses hepatocellular carcinoma initiation and progression by dual inhibition of JAK1/STAT3 and AKT signaling. Cell Rep 2021; 34:108765. [PMID: 33626345 PMCID: PMC7954228 DOI: 10.1016/j.celrep.2021.108765] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 12/07/2020] [Accepted: 01/28/2021] [Indexed: 02/08/2023] Open
Abstract
Hepatocellular carcinoma (HCC) remains one of the deadliest malignancies worldwide. One major obstacle to treatment is a lack of effective molecular-targeted therapies. In this study, we find that EphA2 expression and signaling are enriched in human HCC and associated with poor prognosis. Loss of EphA2 suppresses the initiation and growth of HCC both in vitro and in vivo. Furthermore, CRISPR/CAS9-mediated EphA2 inhibition significantly delays tumor development in a genetically engineered murine model of HCC. Mechanistically, we discover that targeting EphA2 suppresses both AKT and JAK1/STAT3 signaling, two separate oncogenic pathways in HCC. We also identify a small molecule kinase inhibitor of EphA2 that suppresses tumor progression in a murine HCC model. Together, our results suggest EphA2 as a promising therapeutic target for HCC.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Benzamides/pharmacology
- Carcinoma, Hepatocellular/drug therapy
- Carcinoma, Hepatocellular/enzymology
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/pathology
- Cell Line, Tumor
- Databases, Genetic
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Janus Kinase 1/genetics
- Janus Kinase 1/metabolism
- Liver Neoplasms/drug therapy
- Liver Neoplasms/enzymology
- Liver Neoplasms/genetics
- Liver Neoplasms/pathology
- Male
- Mice, Inbred C57BL
- Molecular Targeted Therapy
- Niacinamide/analogs & derivatives
- Niacinamide/pharmacology
- Phosphorylation
- Proto-Oncogene Proteins c-akt/metabolism
- Receptor, EphA2/antagonists & inhibitors
- Receptor, EphA2/genetics
- Receptor, EphA2/metabolism
- Retrospective Studies
- STAT3 Transcription Factor/genetics
- STAT3 Transcription Factor/metabolism
- Signal Transduction
- Tumor Burden/drug effects
- Xenograft Model Antitumor Assays
- Mice
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Affiliation(s)
- Hao Wang
- Department of Surgery, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA; Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Wei Hou
- Department of Surgery, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA; Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Aldeb Perera
- Department of Surgery, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA; Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Carlee Bettler
- Department of Surgery, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA; Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Jordan R Beach
- Department of Cell and Molecular Physiology, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Xianzhong Ding
- Department of Pathology, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Jun Li
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, IN, USA
| | - Mitchell F Denning
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Asha Dhanarajan
- Department of Medicine, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Scott J Cotler
- Department of Medicine, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Cara Joyce
- Department of Public Health Sciences, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Jun Yin
- Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Fowsiyo Ahmed
- Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Wei Qiu
- Department of Surgery, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA; Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA.
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38
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Zhang W, Yang Y, Cui B. New perspectives on the roles of nanoscale surface topography in modulating intracellular signaling. CURRENT OPINION IN SOLID STATE & MATERIALS SCIENCE 2021; 25:100873. [PMID: 33364912 PMCID: PMC7751896 DOI: 10.1016/j.cossms.2020.100873] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The physical properties of biomaterials, such as elasticity, stiffness, and surface nanotopography, are mechanical cues that regulate a broad spectrum of cell behaviors, including migration, differentiation, proliferation, and reprogramming. Among them, nanoscale surface topography, i.e. nanotopography, defines the nanoscale shape and spatial arrangement of surface elements, which directly interact with the cell membranes and stimulate changes in the cell signaling pathways. In biological systems, the effects of nanotopography are often entangled with those of other mechanical and biochemical factors. Precise engineering of 2D nanopatterns and 3D nanostructures with well-defined features has provided a powerful means to study the cellular responses to specific topographic features. In this Review, we discuss efforts in the last three years to understand how nanotopography affects membrane receptor activation, curvature-induced cell signaling, and stem cell differentiation.
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Affiliation(s)
| | | | - Bianxiao Cui
- Department of Chemistry, Stanford University, ChEM-H/Wu Tsai Neuroscience Research Complex, S285, 290 Jane Stanford Way, Stanford, CA, 94305, United States
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39
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Zang Y, Chaudhari K, Bashaw GJ. New insights into the molecular mechanisms of axon guidance receptor regulation and signaling. Curr Top Dev Biol 2021; 142:147-196. [PMID: 33706917 DOI: 10.1016/bs.ctdb.2020.11.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
As the nervous system develops, newly differentiated neurons need to extend their axons toward their synaptic targets to form functional neural circuits. During this highly dynamic process of axon pathfinding, guidance receptors expressed at the tips of motile axons interact with soluble guidance cues or membrane tethered molecules present in the environment to be either attracted toward or repelled away from the source of these cues. As competing cues are often present at the same location and during the same developmental period, guidance receptors need to be both spatially and temporally regulated in order for the navigating axons to make appropriate guidance decisions. This regulation is exerted by a diverse array of molecular mechanisms that have come into focus over the past several decades and these mechanisms ensure that the correct complement of surface receptors is present on the growth cone, a fan-shaped expansion at the tip of the axon. This dynamic, highly motile structure is defined by a lamellipodial network lining the periphery of the growth cone interspersed with finger-like filopodial projections that serve to explore the surrounding environment. Once axon guidance receptors are deployed at the right place and time at the growth cone surface, they respond to their respective ligands by initiating a complex set of signaling events that serve to rearrange the growth cone membrane and the actin and microtubule cytoskeleton to affect axon growth and guidance. In this review, we highlight recent advances that shed light on the rich complexity of mechanisms that regulate axon guidance receptor distribution, activation and downstream signaling.
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Affiliation(s)
- Yixin Zang
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Karina Chaudhari
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Greg J Bashaw
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
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40
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Honig B, Shapiro L. Adhesion Protein Structure, Molecular Affinities, and Principles of Cell-Cell Recognition. Cell 2021; 181:520-535. [PMID: 32359436 DOI: 10.1016/j.cell.2020.04.010] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/25/2020] [Accepted: 04/06/2020] [Indexed: 12/14/2022]
Abstract
The ability of cells to organize into multicellular structures in precise patterns requires that they "recognize" one another with high specificity. We discuss recent progress in understanding the molecular basis of cell-cell recognition, including unique phenomena associated with neuronal interactions. We describe structures of select adhesion receptor complexes and their assembly into larger intercellular junction structures and discuss emerging principles that relate cell-cell organization to the binding specificities and energetics of adhesion receptors. Armed with these insights, advances in protein design and gene editing should pave the way for breakthroughs toward understanding the molecular basis of cell patterning in vivo.
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Affiliation(s)
- Barry Honig
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Medicine, Columbia University, New York, NY 10032, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA.
| | - Lawrence Shapiro
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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41
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Stefanski KM, Russell CM, Westerfield JM, Lamichhane R, Barrera FN. PIP 2 promotes conformation-specific dimerization of the EphA2 membrane region. J Biol Chem 2021; 296:100149. [PMID: 33277361 PMCID: PMC7900517 DOI: 10.1074/jbc.ra120.016423] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/18/2020] [Accepted: 12/04/2020] [Indexed: 12/27/2022] Open
Abstract
The impact of the EphA2 receptor on cancer malignancy hinges on the two different ways it can be activated. EphA2 induces antioncogenic signaling after ligand binding, but ligand-independent activation of EphA2 is pro-oncogenic. It is believed that the transmembrane (TM) domain of EphA2 adopts two alternate conformations in the ligand-dependent and the ligand-independent states. However, it is poorly understood how the difference in TM helical crossing angles found in the two conformations impacts the activity and regulation of EphA2. We devised a method that uses hydrophobic matching to stabilize two conformations of a peptide comprising the EphA2 TM domain and a portion of the intracellular juxtamembrane (JM) segment. The two conformations exhibit different TM crossing angles, resembling the ligand-dependent and ligand-independent states. We developed a single-molecule technique using styrene maleic acid lipid particles to measure dimerization in membranes. We observed that the signaling lipid PIP2 promotes TM dimerization, but only in the small crossing angle state, which we propose corresponds to the ligand-independent conformation. In this state the two TMs are almost parallel, and the positively charged JM segments are expected to be close to each other, causing electrostatic repulsion. The mechanism PIP2 uses to promote dimerization might involve alleviating this repulsion due to its high density of negative charges. Our data reveal a conformational coupling between the TM and JM regions and suggest that PIP2 might directly exert a regulatory effect on EphA2 activation in cells that is specific to the ligand-independent conformation of the receptor.
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Affiliation(s)
- Katherine M Stefanski
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, USA
| | - Charles M Russell
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
| | - Justin M Westerfield
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
| | - Rajan Lamichhane
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA.
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA.
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42
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Liu Y, Ribeiro ODC, Robinson J, Goldman A. Expression and purification of the extracellular domain of wild-type humanRET and the dimeric oncogenic mutant C634R. Int J Biol Macromol 2020; 164:1621-1630. [PMID: 32777409 DOI: 10.1016/j.ijbiomac.2020.07.290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/15/2020] [Accepted: 07/24/2020] [Indexed: 12/01/2022]
Abstract
The receptor tyrosine kinase RET is essential in a variety of cellular processes. RET gain-of-function is strongly associated with several cancers, notably multiple endocrine neoplasia type 2A (MEN 2A), while RET loss-of-function causes Hirschsprung's disease and Parkinson's disease. To investigate the activation mechanism of RET as well as to enable drug development, over-expressed recombinant protein is needed for in vitro functional and structural studies. By comparing insect and mammalian cells expression of the RET extracellular domain (RETECD), we showed that the expression yields of RETECD using both systems were comparable, but mammalian cells produced monomeric functional RETECD, whereas RETECD expressed in insect cells was non-functional and multimeric. This was most likely due to incorrect disulfide formation. By fusing an Fc tag to the C-terminus of RETECD, we were able to produce, in HEK293T cells, dimeric oncogenic RETECD (C634R) for the first time. The protein remained dimeric even after cleavage of the tag via the cysteine disulfide, as in full-length RET in the context of MEN 2A and related pathologies. Our work thus provides valuable tools for functional and structural studies of the RET signaling system and its oncogenic activation mechanisms.
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Affiliation(s)
- Yixin Liu
- Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki 00790, Finland
| | - Orquidea De Castro Ribeiro
- Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki 00790, Finland
| | - James Robinson
- Discovery and Translational Sciences Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Adrian Goldman
- Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki 00790, Finland; Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK.
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43
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Su C, Wu L, Chai Y, Qi J, Tan S, Gao GF, Song H, Yan J. Molecular basis of EphA2 recognition by gHgL from gammaherpesviruses. Nat Commun 2020; 11:5964. [PMID: 33235207 PMCID: PMC7687889 DOI: 10.1038/s41467-020-19617-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/19/2020] [Indexed: 01/07/2023] Open
Abstract
The human γ-herpesviruses Kaposi sarcoma associated herpesvirus (KSHV) and Epstein-Barr virus (EBV) are associated with many human malignancies. Viral glycoprotein H (gH) and glycoprotein L (gL) are crucial for the cell tropism by binding to specific receptors. Recently, EphA2 was identified as the specific entry receptor for both KSHV and EBV. Here, we characterized the crystal structures of KSHV gHgL or EBV gHgL in complex with the ligand binding domain (LBD) of EphA2. Both KSHV and EBV gHgL bind to the channel and peripheral regions of LBD primarily using gL. Extensive interactions with more contacts contribute to the higher affinity of KSHV gHgL to LBD than that of EBV gHgL. These binding characteristics were verified using cell-based fusion assays with mutations in key EphA2 residues. Our experiments suggest that multiple animal γ-herpesviruses could use EphA2 as an entry receptor, implying a potential threat to human health.
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Affiliation(s)
- Chao Su
- grid.22935.3f0000 0004 0530 8290College of Veterinary Medicine, China Agricultural University, Beijing, 100193 China
| | - Lili Wu
- grid.9227.e0000000119573309CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yan Chai
- grid.9227.e0000000119573309CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Jianxun Qi
- grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China ,grid.9227.e0000000119573309CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Shuguang Tan
- grid.9227.e0000000119573309CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - George F. Gao
- grid.22935.3f0000 0004 0530 8290College of Veterinary Medicine, China Agricultural University, Beijing, 100193 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China ,grid.9227.e0000000119573309CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.9227.e0000000119573309Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101 China
| | - Hao Song
- grid.9227.e0000000119573309Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101 China
| | - Jinghua Yan
- grid.9227.e0000000119573309CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
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44
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Zhang W, Mo S, Liu M, Liu L, Yu L, Wang C. Rationally Designed Protein Building Blocks for Programmable Hierarchical Architectures. Front Chem 2020; 8:587975. [PMID: 33195088 PMCID: PMC7658299 DOI: 10.3389/fchem.2020.587975] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/05/2020] [Indexed: 01/23/2023] Open
Abstract
Diverse natural/artificial proteins have been used as building blocks to construct a variety of well-ordered nanoscale structures over the past couple of decades. Sophisticated protein self-assemblies have attracted great scientific interests due to their potential applications in disease diagnosis, illness treatment, biomechanics, bio-optics and bio-electronics, etc. This review outlines recent efforts directed to the creation of structurally defined protein assemblies including one-dimensional (1D) strings/rings/tubules, two-dimensional (2D) planar sheets and three-dimensional (3D) polyhedral scaffolds. We elucidate various innovative strategies for manipulating proteins to self-assemble into desired architectures. The emergent applications of protein assemblies as versatile platforms in medicine and material science with improved performances have also been discussed.
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Affiliation(s)
- Wenbo Zhang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shanshan Mo
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mingwei Liu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lei Liu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Lanlan Yu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chenxuan Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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45
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Rochman ND, Wolf YI, Koonin EV. Deep phylogeny of cancer drivers and compensatory mutations. Commun Biol 2020; 3:551. [PMID: 33009502 PMCID: PMC7532533 DOI: 10.1038/s42003-020-01276-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/03/2020] [Indexed: 12/14/2022] Open
Abstract
Driver mutations (DM) are the genetic impetus for most cancers. The DM are assumed to be deleterious in species evolution, being eliminated by purifying selection unless compensated by other mutations. We present deep phylogenies for 84 cancer driver genes and investigate the prevalence of 434 DM across gene-species trees. The DM are rare in species evolution, and 181 are completely absent, validating their negative fitness effect. The DM are more common in unicellular than in multicellular eukaryotes, suggesting a link between these mutations and cell proliferation control. 18 DM appear as the ancestral state in one or more major clades, including 3 among mammals. We identify within-gene, compensatory mutations for 98 DM and infer likely interactions between the DM and compensatory sites in protein structures. These findings elucidate the evolutionary status of DM and are expected to advance the understanding of the functions and evolution of oncogenes and tumor suppressors. Rochman et al. present deep phylogenies for 84 cancer driver genes and examine the prevalence of driver mutations across gene-species trees. Their results show that driver mutations are rare in species evolution and give insight into the evolution of driver mutations and oncogenes.
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Affiliation(s)
- Nash D Rochman
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.
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46
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Shrestha S, Byrne DP, Harris JA, Kannan N, Eyers PA. Cataloguing the dead: breathing new life into pseudokinase research. FEBS J 2020; 287:4150-4169. [PMID: 32053275 PMCID: PMC7586955 DOI: 10.1111/febs.15246] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/22/2020] [Accepted: 02/11/2020] [Indexed: 12/22/2022]
Abstract
Pseudoenzymes are present within many, but not all, known enzyme families and lack one or more conserved canonical amino acids that help define their catalytically active counterparts. Recent findings in the pseudokinase field confirm that evolutionary repurposing of the structurally defined bilobal protein kinase fold permits distinct biological functions to emerge, many of which rely on conformational switching, as opposed to canonical catalysis. In this analysis, we evaluate progress in evaluating several members of the 'dark' pseudokinome that are pertinent to help drive this expanding field. Initially, we discuss how adaptions in erythropoietin-producing hepatocellular carcinoma (Eph) receptor tyrosine kinase domains resulted in two vertebrate pseudokinases, EphA10 and EphB6, in which co-evolving sequences generate new motifs that are likely to be important for both nucleotide binding and catalysis-independent signalling. Secondly, we discuss how conformationally flexible Tribbles pseudokinases, which have radiated in the complex vertebrates, control fundamental aspects of cell signalling that may be targetable with covalent small molecules. Finally, we show how species-level adaptions in the duplicated canonical kinase protein serine kinase histone (PSKH)1 sequence have led to the appearance of the pseudokinase PSKH2, whose physiological role remains mysterious. In conclusion, we show how the patterns we discover are selectively conserved within specific pseudokinases, and that when they are modelled alongside closely related canonical kinases, many are found to be located in functionally important regions of the conserved kinase fold. Interrogation of these patterns will be useful for future evaluation of these, and other, members of the unstudied human kinome.
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Affiliation(s)
- Safal Shrestha
- Institute of BioinformaticsUniversity of GeorgiaAthensGAUSA
- Department of Biochemistry & Molecular BiologyUniversity of GeorgiaAthensGAUSA
| | - Dominic P. Byrne
- Department of BiochemistryInstitute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - John A. Harris
- Department of BiochemistryInstitute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Natarajan Kannan
- Institute of BioinformaticsUniversity of GeorgiaAthensGAUSA
- Department of Biochemistry & Molecular BiologyUniversity of GeorgiaAthensGAUSA
| | - Patrick A. Eyers
- Department of BiochemistryInstitute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
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47
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Xiao T, Xiao Y, Wang W, Tang YY, Xiao Z, Su M. Targeting EphA2 in cancer. J Hematol Oncol 2020; 13:114. [PMID: 32811512 PMCID: PMC7433191 DOI: 10.1186/s13045-020-00944-9] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/27/2020] [Indexed: 12/18/2022] Open
Abstract
Eph receptors and the corresponding Eph receptor-interacting (ephrin) ligands jointly constitute a critical cell signaling network that has multiple functions. The tyrosine kinase EphA2, which belongs to the family of Eph receptors, is highly produced in tumor tissues, while found at relatively low levels in most normal adult tissues, indicating its potential application in cancer treatment. After 30 years of investigation, a large amount of data regarding EphA2 functions have been compiled. Meanwhile, several compounds targeting EphA2 have been evaluated and tested in clinical studies, albeit with limited clinical success. The present review briefly describes the contribution of EphA2-ephrin A1 signaling axis to carcinogenesis. In addition, the roles of EphA2 in resistance to molecular-targeted agents were examined. In particular, we focused on EphA2's potential as a target for cancer treatment to provide insights into the application of EphA2 targeting in anticancer strategies. Overall, EphA2 represents a potential target for treating malignant tumors.
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Affiliation(s)
- Ta Xiao
- Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, 210042, China
| | - Yuhang Xiao
- Research Center of Carcinogenesis and Targeted Therapy, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Wenxiang Wang
- Thoracic Surgery Department 2, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, China.,Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Yan Yan Tang
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Zhiqiang Xiao
- Research Center of Carcinogenesis and Targeted Therapy, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Min Su
- Thoracic Surgery Department 2, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, China. .,Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China.
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48
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Verheyen T, Fang T, Lindenhofer D, Wang Y, Akopyan K, Lindqvist A, Högberg B, Teixeira AI. Spatial organization-dependent EphA2 transcriptional responses revealed by ligand nanocalipers. Nucleic Acids Res 2020; 48:5777-5787. [PMID: 32352518 PMCID: PMC7261182 DOI: 10.1093/nar/gkaa274] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 04/01/2020] [Accepted: 04/08/2020] [Indexed: 11/13/2022] Open
Abstract
Ligand binding induces extensive spatial reorganization and clustering of the EphA2 receptor at the cell membrane. It has previously been shown that the nanoscale spatial distribution of ligands modulates EphA2 receptor reorganization, activation and the invasive properties of cancer cells. However, intracellular signaling downstream of EphA2 receptor activation by nanoscale spatially distributed ligands has not been elucidated. Here, we used DNA origami nanostructures to control the positions of ephrin-A5 ligands at the nanoscale and investigated EphA2 activation and transcriptional responses following ligand binding. Using RNA-seq, we determined the transcriptional profiles of human glioblastoma cells treated with DNA nanocalipers presenting a single ephrin-A5 dimer or two dimers spaced 14, 40 or 100 nm apart. These cells displayed divergent transcriptional responses to the differing ephrin-A5 nano-organization. Specifically, ephrin-A5 dimers spaced 40 or 100 nm apart showed the highest levels of differential expressed genes compared to treatment with nanocalipers that do not present ephrin-A5. These findings show that the nanoscale organization of ephrin-A5 modulates transcriptional responses to EphA2 activation.
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Affiliation(s)
- Toon Verheyen
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm 17165, Sweden
| | - Trixy Fang
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm 17165, Sweden
| | - Dominik Lindenhofer
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm 17165, Sweden
| | - Yang Wang
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm 17165, Sweden
| | - Karen Akopyan
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm 17165, Sweden
| | - Arne Lindqvist
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm 17165, Sweden
| | - Björn Högberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm 17165, Sweden
| | - Ana I Teixeira
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm 17165, Sweden
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49
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Ravasio A, Myaing MZ, Chia S, Arora A, Sathe A, Cao EY, Bertocchi C, Sharma A, Arasi B, Chung VY, Greene AC, Tan TZ, Chen Z, Ong HT, Iyer NG, Huang RY, DasGupta R, Groves JT, Viasnoff V. Single-cell analysis of EphA clustering phenotypes to probe cancer cell heterogeneity. Commun Biol 2020; 3:429. [PMID: 32764731 PMCID: PMC7411022 DOI: 10.1038/s42003-020-01136-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 06/29/2020] [Indexed: 11/28/2022] Open
Abstract
The Eph family of receptor tyrosine kinases is crucial for assembly and maintenance of healthy tissues. Dysfunction in Eph signaling is causally associated with cancer progression. In breast cancer cells, dysregulated Eph signaling has been linked to alterations in receptor clustering abilities. Here, we implemented a single-cell assay and a scoring scheme to systematically probe the spatial organization of activated EphA receptors in multiple carcinoma cells. We show that cancer cells retain EphA clustering phenotype over several generations, and the degree of clustering reported for migration potential both at population and single-cell levels. Finally, using patient-derived cancer lines, we probed the evolution of EphA signalling in cell populations that underwent metastatic transformation and acquisition of drug resistance. Taken together, our scalable approach provides a reliable scoring scheme for EphA clustering that is consistent over multiple carcinomas and can assay heterogeneity of cancer cell populations in a cost- and time-effective manner. Ravasio et al. develop an assay to quantify the clustering of Eph receptor EphA2 upon ligand binding, based on the scoring of single cells. They discover that clustering phenotype predicts cell and population migration potential in cancer cells and reflects Eph associated gene expression profiles in cancer cell lines.
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Affiliation(s)
- Andrea Ravasio
- National University of Singapore, Singapore, Singapore.,Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Shumei Chia
- Genome Institute of Singapore, A-STAR, Singapore, Singapore
| | - Aditya Arora
- National University of Singapore, Singapore, Singapore
| | - Aneesh Sathe
- National University of Singapore, Singapore, Singapore
| | | | - Cristina Bertocchi
- National University of Singapore, Singapore, Singapore.,Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ankur Sharma
- Genome Institute of Singapore, A-STAR, Singapore, Singapore
| | - Bakya Arasi
- National University of Singapore, Singapore, Singapore
| | - Vin Yee Chung
- National University of Singapore, Singapore, Singapore
| | | | - Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Zhongwen Chen
- National University of Singapore, Singapore, Singapore
| | - Hui Ting Ong
- National University of Singapore, Singapore, Singapore
| | | | - Ruby YunJu Huang
- School of Medicine & Graduate Institute of Oncology, College of Medicine, National Taiwan, Taiwan.,University Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - Jay T Groves
- National University of Singapore, Singapore, Singapore.,University of California, Berkeley, CA, USA
| | - Virgile Viasnoff
- National University of Singapore, Singapore, Singapore. .,Centre National de la Recherche Scientifique, Singapore, Singapore.
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50
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Baudet S, Bécret J, Nicol X. Approaches to Manipulate Ephrin-A:EphA Forward Signaling Pathway. Pharmaceuticals (Basel) 2020; 13:ph13070140. [PMID: 32629797 PMCID: PMC7407804 DOI: 10.3390/ph13070140] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/19/2020] [Accepted: 06/28/2020] [Indexed: 02/07/2023] Open
Abstract
Erythropoietin-producing hepatocellular carcinoma A (EphA) receptors and their ephrin-A ligands are key players of developmental events shaping the mature organism. Their expression is mostly restricted to stem cell niches in adults but is reactivated in pathological conditions including lesions in the heart, lung, or nervous system. They are also often misregulated in tumors. A wide range of molecular tools enabling the manipulation of the ephrin-A:EphA system are available, ranging from small molecules to peptides and genetically-encoded strategies. Their mechanism is either direct, targeting EphA receptors, or indirect through the modification of intracellular downstream pathways. Approaches enabling manipulation of ephrin-A:EphA forward signaling for the dissection of its signaling cascade, the investigation of its physiological roles or the development of therapeutic strategies are summarized here.
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