1
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Cabral G, Moss WJ, Brown KM. Proteomic approaches for protein kinase substrate identification in Apicomplexa. Mol Biochem Parasitol 2024; 259:111633. [PMID: 38821187 PMCID: PMC11194964 DOI: 10.1016/j.molbiopara.2024.111633] [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: 03/30/2024] [Revised: 05/10/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
Apicomplexa is a phylum of protist parasites, notable for causing life-threatening diseases including malaria, toxoplasmosis, cryptosporidiosis, and babesiosis. Apicomplexan pathogenesis is generally a function of lytic replication, dissemination, persistence, host cell modification, and immune subversion. Decades of research have revealed essential roles for apicomplexan protein kinases in establishing infections and promoting pathogenesis. Protein kinases modify their substrates by phosphorylating serine, threonine, tyrosine, or other residues, resulting in rapid functional changes in the target protein. Post-translational modification by phosphorylation can activate or inhibit a substrate, alter its localization, or promote interactions with other proteins or ligands. Deciphering direct kinase substrates is crucial to understand mechanisms of kinase signaling, yet can be challenging due to the transient nature of kinase phosphorylation and potential for downstream indirect phosphorylation events. However, with recent advances in proteomic approaches, our understanding of kinase function in Apicomplexa has improved dramatically. Here, we discuss methods that have been used to identify kinase substrates in apicomplexan parasites, classifying them into three main categories: i) kinase interactome, ii) indirect phosphoproteomics and iii) direct labeling. We briefly discuss each approach, including their advantages and limitations, and highlight representative examples from the Apicomplexa literature. Finally, we conclude each main category by introducing prospective approaches from other fields that would benefit kinase substrate identification in Apicomplexa.
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Affiliation(s)
- Gabriel Cabral
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - William J Moss
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kevin M Brown
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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2
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Guillet S, Lazarov T, Jordan N, Boisson B, Tello M, Craddock B, Zhou T, Nishi C, Bareja R, Yang H, Rieux-Laucat F, Lorenzo RIF, Dyall SD, Isenberg D, D’Cruz D, Lachmann N, Elemento O, Viale A, Socci ND, Abel L, Nagata S, Huse M, Miller WT, Casanova JL, Geissmann F. ACK1 and BRK non-receptor tyrosine kinase deficiencies are associated with familial systemic lupus and involved in efferocytosis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.15.24302255. [PMID: 38883731 PMCID: PMC11177913 DOI: 10.1101/2024.02.15.24302255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Systemic Lupus Erythematosus (SLE) is an autoimmune disease, the pathophysiology and genetic basis of which are incompletely understood. Using a forward genetic screen in multiplex families with systemic lupus erythematosus (SLE) we identified an association between SLE and compound heterozygous deleterious variants in the non-receptor tyrosine kinases (NRTKs) ACK1 and BRK. Experimental blockade of ACK1 or BRK increased circulating autoantibodies in vivo in mice and exacerbated glomerular IgG deposits in an SLE mouse model. Mechanistically, non-receptor tyrosine kinases (NRTKs) regulate activation, migration, and proliferation of immune cells. We found that the patients' ACK1 and BRK variants impair efferocytosis, the MERTK-mediated anti-inflammatory response to apoptotic cells, in human induced Pluripotent Stem Cell (hiPSC)-derived macrophages, which may contribute to SLE pathogenesis. Overall, our data suggest that ACK1 and BRK deficiencies are associated with human SLE and impair efferocytosis in macrophages.
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Affiliation(s)
- Stephanie Guillet
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Ecole doctorale Bio Sorbonne Paris Cité, Université Paris Descartes-Sorbonne Paris Cité.Paris, France
| | - Tomi Lazarov
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of MedicalSciences, New York, New York 10065, USA
| | - Natasha Jordan
- Centre for Molecular and Cellular Biology of Inflammation (CMCBI), King’s College London and Louise Coote Lupus Unit, Guy’s and Thomas’ Hospitals, London SE1 1UL, UK
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, 10065 NY, USA
- University of Paris Cité, Imagine Institute, Paris, France
| | - Maria Tello
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Barbara Craddock
- Department of Physiology and Biophysics, Stony Brook University School of Medicine, Stony Brook, NY, 11794-8661
| | - Ting Zhou
- SKI Stem Cell Research Core, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Chihiro Nishi
- Laboratory of Biochemistry & Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871
| | - Rohan Bareja
- Cary and Israel Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Meyer Cancer Center Weill Cornell Medical College, New York, New York 10065, USA
| | - Hairu Yang
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | | | | | - Sabrina D. Dyall
- Department of Biosciences and Ocean Studies, Faculty of Science, University of Mauritius, Reduit, Mauritius
| | - David Isenberg
- Centre for Rheumatology, Division of Medicine, University College London, The Rayne Building, University College London
| | - David D’Cruz
- Centre for Molecular and Cellular Biology of Inflammation (CMCBI), King’s College London and Louise Coote Lupus Unit, Guy’s and Thomas’ Hospitals, London SE1 1UL, UK
| | - Nico Lachmann
- Institute of Experimental Hematology, REBIRTH Cluster of Excellence, Hannover Medical School, Hannover 30625, Germany
| | - Olivier Elemento
- Cary and Israel Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Meyer Cancer Center Weill Cornell Medical College, New York, New York 10065, USA
| | - Agnes Viale
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Nicholas D. Socci
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, 10065 NY, USA
- University of Paris Cité, Imagine Institute, Paris, France
| | - Shigekazu Nagata
- Laboratory of Biochemistry & Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871
| | - Morgan Huse
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - W. Todd Miller
- Department of Physiology and Biophysics, Stony Brook University School of Medicine, Stony Brook, NY, 11794-8661
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, 10065 NY, USA
- University of Paris Cité, Imagine Institute, Paris, France
- Howard Hughes Medical Institute, New York, 10065 NY, USA
- Lab of Human Genetics of Infectious Diseases, INSERM, Necker Hospital for Sick Children, Paris, France, EU
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France, EU
| | - Frederic Geissmann
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of MedicalSciences, New York, New York 10065, USA
- Centre for Molecular and Cellular Biology of Inflammation (CMCBI), King’s College London and Louise Coote Lupus Unit, Guy’s and Thomas’ Hospitals, London SE1 1UL, UK
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3
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Weng Y, Chen W, Kong Q, Wang R, Zeng R, He A, Liu Y, Mao Y, Qin Y, Ngai WSC, Zhang H, Ke M, Wang J, Tian R, Chen PR. DeKinomics pulse-chases kinase functions in living cells. Nat Chem Biol 2024; 20:615-623. [PMID: 38167916 DOI: 10.1038/s41589-023-01497-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 11/02/2023] [Indexed: 01/05/2024]
Abstract
Cellular context is crucial for understanding the complex and dynamic kinase functions in health and disease. Systematic dissection of kinase-mediated cellular processes requires rapid and precise stimulation ('pulse') of a kinase of interest, as well as global and in-depth characterization ('chase') of the perturbed proteome under living conditions. Here we developed an optogenetic 'pulse-chase' strategy, termed decaging kinase coupled proteomics (DeKinomics), for proteome-wide profiling of kinase-driven phosphorylation at second-timescale in living cells. We took advantage of the 'gain-of-function' feature of DeKinomics to identify direct kinase substrates and further portrayed the global phosphorylation of understudied receptor tyrosine kinases under native cellular settings. DeKinomics offered a general activation-based strategy to study kinase functions with high specificity and temporal resolution under living conditions.
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Affiliation(s)
- Yicheng Weng
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, New Cornerstone Science Laboratory, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Wendong Chen
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, China
- South China Institute of Biomedicine, Academy of Phronesis Medicine, Guangzhou, China
| | - Qian Kong
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, China
| | - Ruixiang Wang
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, New Cornerstone Science Laboratory, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Ruxin Zeng
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, New Cornerstone Science Laboratory, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - An He
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, China
| | - Yanjun Liu
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, New Cornerstone Science Laboratory, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Yiheng Mao
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, China
| | - Yunqiu Qin
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, China
| | | | - Heng Zhang
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Mi Ke
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, China
| | - Jie Wang
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, China
| | - Ruijun Tian
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, China.
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, China.
| | - Peng R Chen
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, New Cornerstone Science Laboratory, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- Shenzhen Bay Laboratory, Shenzhen, China.
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4
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Sennett MA, Theobald DL. Extant Sequence Reconstruction: The Accuracy of Ancestral Sequence Reconstructions Evaluated by Extant Sequence Cross-Validation. J Mol Evol 2024; 92:181-206. [PMID: 38502220 PMCID: PMC10978691 DOI: 10.1007/s00239-024-10162-3] [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: 07/12/2023] [Accepted: 02/20/2024] [Indexed: 03/21/2024]
Abstract
Ancestral sequence reconstruction (ASR) is a phylogenetic method widely used to analyze the properties of ancient biomolecules and to elucidate mechanisms of molecular evolution. Despite its increasingly widespread application, the accuracy of ASR is currently unknown, as it is generally impossible to compare resurrected proteins to the true ancestors. Which evolutionary models are best for ASR? How accurate are the resulting inferences? Here we answer these questions using a cross-validation method to reconstruct each extant sequence in an alignment with ASR methodology, a method we term "extant sequence reconstruction" (ESR). We thus can evaluate the accuracy of ASR methodology by comparing ESR reconstructions to the corresponding known true sequences. We find that a common measure of the quality of a reconstructed sequence, the average probability, is indeed a good estimate of the fraction of correct amino acids when the evolutionary model is accurate or overparameterized. However, the average probability is a poor measure for comparing reconstructions from different models, because, surprisingly, a more accurate phylogenetic model often results in reconstructions with lower probability. While better (more predictive) models may produce reconstructions with lower sequence identity to the true sequences, better models nevertheless produce reconstructions that are more biophysically similar to true ancestors. In addition, we find that a large fraction of sequences sampled from the reconstruction distribution may have fewer errors than the single most probable (SMP) sequence reconstruction, despite the fact that the SMP has the lowest expected error of all possible sequences. Our results emphasize the importance of model selection for ASR and the usefulness of sampling sequence reconstructions for analyzing ancestral protein properties. ESR is a powerful method for validating the evolutionary models used for ASR and can be applied in practice to any phylogenetic analysis of real biological sequences. Most significantly, ESR uses ASR methodology to provide a general method by which the biophysical properties of resurrected proteins can be compared to the properties of the true protein.
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Affiliation(s)
- Michael A Sennett
- Department of Biochemistry, Brandeis University, Waltham, MA, 02453, USA
| | - Douglas L Theobald
- Department of Biochemistry, Brandeis University, Waltham, MA, 02453, USA.
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5
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Kim Y, Miller WT. Contrasting Effects of Cancer-Associated Mutations in EphA3 and EphB2 Kinases. Biochemistry 2024. [PMID: 38252844 DOI: 10.1021/acs.biochem.3c00674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Erythropoietin-producing hepatoma (Eph) receptors are a family of tyrosine kinases that can act as tumor promoters or tumor suppressors, depending on the receptor and cancer cell type. Cancer-associated somatic mutations have been identified in all Eph receptors, but in most cases, the functional effects of the mutations are unknown. In this study, we expressed and purified the kinase domains of wild-type (WT) EphA3 and EphB2 along with 16 cancer-associated mutants. We identified mutations that decrease EphA3 activity and both activating and inhibitory mutations in EphB2. To shed light on the mechanisms by which the mutations altered kinase activity, we measured the thermal stabilities of the enzymes and performed steady-state kinetic experiments. We also expressed the full-length receptors in HEK293T cells to determine the cellular effects. WT EphB2 promoted downstream ERK signaling, while a kinase-inactive mutant (S706F) was similar to the control cells. In contrast, WT EphA3 (but not loss-of-function mutants) inhibited ERK signaling. The reciprocal effects of EphB2 and EphA3 on ERK phosphorylation in HEK293T cells were also evident in Ras-GTP loading. Thus, consistent with the dual roles of Eph receptors as tumor promoters and tumor suppressors, somatic mutations have the potential to increase or decrease Eph function, resulting in changes in the downstream signaling transduction.
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Affiliation(s)
- Yunyoung Kim
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794, United States
| | - W Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Veterans Affairs Medical Center, Northport, New York 11768, United States
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6
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Krishnan H, Ahmed S, Hubbard SR, Miller WT. Biochemical characterization of the Drosophila insulin receptor kinase and longevity-associated mutants. FASEB J 2024; 38:e23355. [PMID: 38071609 DOI: 10.1096/fj.202301948r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/13/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023]
Abstract
Drosophila melanogaster (fruit fly) insulin receptor (D-IR) is highly homologous to the human counterpart. Like the human pathway, D-IR responds to numerous insulin-like peptides to activate cellular signals that regulate growth, development, and lipid metabolism in fruit flies. Allelic mutations in the D-IR kinase domain elevate life expectancy in fruit flies. We developed a robust heterologous expression system to express and purify wild-type and longevity-associated mutant D-IR kinase domains to investigate enzyme kinetics and substrate specificities. D-IR exhibits remarkable similarities to the human insulin receptor kinase domain but diverges in substrate preferences. We show that longevity-associated mutations reduce D-IR catalytic activity. Deletion of the unique kinase insert domain portion or mutations proximal to activating tyrosines do not influence kinase activity, suggesting their potential role in substrate recruitment and downstream signaling. Through biochemical investigations, this study enhances our comprehension of D-IR's role in Drosophila physiology, complementing genetic studies and expanding our knowledge on the catalytic functions of this conserved signaling pathway.
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Affiliation(s)
- Harini Krishnan
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Sultan Ahmed
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Stevan R Hubbard
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
| | - W Todd Miller
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York, USA
- Department of Veterans Affairs Medical Center, Northport, New York, USA
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7
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Kim Y, Ahmed S, Miller WT. Colorectal cancer-associated mutations impair EphB1 kinase function. J Biol Chem 2023; 299:105115. [PMID: 37527777 PMCID: PMC10463257 DOI: 10.1016/j.jbc.2023.105115] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023] Open
Abstract
Erythropoietin-producing hepatoma (Eph) receptor tyrosine kinases regulate the migration and adhesion of cells that are required for many developmental processes and adult tissue homeostasis. In the intestinal epithelium, Eph signaling controls the positioning of cell types along the crypt-villus axis. Eph activity can suppress the progression of colorectal cancer (CRC). The most frequently mutated Eph receptor in metastatic CRC is EphB1. However, the functional effects of EphB1 mutations are mostly unknown. We expressed and purified the kinase domains of WT and five cancer-associated mutant EphB1 and developed assays to assess the functional effects of the mutations. Using purified proteins, we determined that CRC-associated mutations reduce the activity and stability of the folded structure of EphB1. By mammalian cell expression, we determined that CRC-associated mutant EphB1 receptors inhibit signal transducer and activator of transcription 3 and extracellular signal-regulated kinases 1 and 2 signaling. In contrast to the WT, the mutant EphB1 receptors are unable to suppress the migration of human CRC cells. The CRC-associated mutations also impair cell compartmentalization in an assay in which EphB1-expressing cells are cocultured with ligand (ephrin B1)-expressing cells. These results suggest that somatic mutations impair the kinase-dependent tumor suppressor function of EphB1 in CRC.
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Affiliation(s)
- Yunyoung Kim
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA
| | - Sultan Ahmed
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA
| | - W Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA; Department of Veterans Affairs Medical Center, Northport, New York, USA.
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8
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Geffen Y, Anand S, Akiyama Y, Yaron TM, Song Y, Johnson JL, Govindan A, Babur Ö, Li Y, Huntsman E, Wang LB, Birger C, Heiman DI, Zhang Q, Miller M, Maruvka YE, Haradhvala NJ, Calinawan A, Belkin S, Kerelsky A, Clauser KR, Krug K, Satpathy S, Payne SH, Mani DR, Gillette MA, Dhanasekaran SM, Thiagarajan M, Mesri M, Rodriguez H, Robles AI, Carr SA, Lazar AJ, Aguet F, Cantley LC, Ding L, Getz G. Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation. Cell 2023; 186:3945-3967.e26. [PMID: 37582358 PMCID: PMC10680287 DOI: 10.1016/j.cell.2023.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 01/06/2023] [Accepted: 07/10/2023] [Indexed: 08/17/2023]
Abstract
Post-translational modifications (PTMs) play key roles in regulating cell signaling and physiology in both normal and cancer cells. Advances in mass spectrometry enable high-throughput, accurate, and sensitive measurement of PTM levels to better understand their role, prevalence, and crosstalk. Here, we analyze the largest collection of proteogenomics data from 1,110 patients with PTM profiles across 11 cancer types (10 from the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium [CPTAC]). Our study reveals pan-cancer patterns of changes in protein acetylation and phosphorylation involved in hallmark cancer processes. These patterns revealed subsets of tumors, from different cancer types, including those with dysregulated DNA repair driven by phosphorylation, altered metabolic regulation associated with immune response driven by acetylation, affected kinase specificity by crosstalk between acetylation and phosphorylation, and modified histone regulation. Overall, this resource highlights the rich biology governed by PTMs and exposes potential new therapeutic avenues.
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Affiliation(s)
- Yifat Geffen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA
| | - Shankara Anand
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Yo Akiyama
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Tomer M Yaron
- Weill Cornell Medical College, Meyer Cancer Center, New York, NY 10021, USA
| | - Yizhe Song
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jared L Johnson
- Weill Cornell Medical College, Meyer Cancer Center, New York, NY 10021, USA
| | - Akshay Govindan
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Özgün Babur
- Department of Computer Science, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Yize Li
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Emily Huntsman
- Weill Cornell Medical College, Meyer Cancer Center, New York, NY 10021, USA
| | - Liang-Bo Wang
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chet Birger
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - David I Heiman
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Qing Zhang
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Mendy Miller
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Yosef E Maruvka
- Biotechnology and Food Engineering, Lokey Center for Life Science and Engineering, Technion, Israel Institute of Technology, Haifa, Israel
| | - Nicholas J Haradhvala
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Anna Calinawan
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Saveliy Belkin
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Alexander Kerelsky
- Weill Cornell Medical College, Meyer Cancer Center, New York, NY 10021, USA
| | - Karl R Clauser
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Michael A Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA
| | | | - Mathangi Thiagarajan
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Steven A Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Alexander J Lazar
- Departments of Pathology & Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - François Aguet
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
| | - Lewis C Cantley
- Weill Cornell Medical College, Meyer Cancer Center, New York, NY 10021, USA.
| | - Li Ding
- Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Gad Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
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9
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Chessa TAM, Jung P, Anwar A, Suire S, Anderson KE, Barneda D, Kielkowska A, Sadiq BA, Lai IW, Felisbino S, Turnham DJ, Pearson HB, Phillips WA, Sasaki J, Sasaki T, Oxley D, Spensberger D, Segonds-Pichon A, Wilson M, Walker S, Okkenhaug H, Cosulich S, Hawkins PT, Stephens LR. PLEKHS1 drives PI3Ks and remodels pathway homeostasis in PTEN-null prostate. Mol Cell 2023; 83:2991-3009.e13. [PMID: 37567175 DOI: 10.1016/j.molcel.2023.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 05/05/2023] [Accepted: 07/13/2023] [Indexed: 08/13/2023]
Abstract
The PIP3/PI3K network is a central regulator of metabolism and is frequently activated in cancer, commonly by loss of the PIP3/PI(3,4)P2 phosphatase, PTEN. Despite huge research investment, the drivers of the PI3K network in normal tissues and how they adapt to overactivation are unclear. We find that in healthy mouse prostate PI3K activity is driven by RTK/IRS signaling and constrained by pathway feedback. In the absence of PTEN, the network is dramatically remodeled. A poorly understood YXXM- and PIP3/PI(3,4)P2-binding PH domain-containing adaptor, PLEKHS1, became the dominant activator and was required to sustain PIP3, AKT phosphorylation, and growth in PTEN-null prostate. This was because PLEKHS1 evaded pathway-feedback and experienced enhanced PI3K- and Src-family kinase-dependent phosphorylation of Y258XXM, eliciting PI3K activation. hPLEKHS1 mRNA and activating Y419 phosphorylation of hSrc correlated with PI3K pathway activity in human prostate cancers. We propose that in PTEN-null cells receptor-independent, Src-dependent tyrosine phosphorylation of PLEKHS1 creates positive feedback that escapes homeostasis, drives PIP3 signaling, and supports tumor progression.
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Affiliation(s)
| | - Piotr Jung
- Signalling Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Arqum Anwar
- Signalling Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Sabine Suire
- Signalling Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Karen E Anderson
- Signalling Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - David Barneda
- Signalling Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Anna Kielkowska
- Signalling Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Barzan A Sadiq
- Signalling Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Ieng Wai Lai
- Signalling Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Sergio Felisbino
- Department of Structural and Functional Biology, São Paulo State University, Botucatu, SP CEP: 18618-689, Brazil
| | - Daniel J Turnham
- European Cancer Stem Cell Research Institute, Cardiff University, Cardiff CF24 4HQ, UK
| | - Helen B Pearson
- European Cancer Stem Cell Research Institute, Cardiff University, Cardiff CF24 4HQ, UK
| | - Wayne A Phillips
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Junko Sasaki
- Department of Biochemical Pathophysiology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Takehiko Sasaki
- Department of Biochemical Pathophysiology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - David Oxley
- Mass Spectrometry Facility, Babraham Institute, Cambridge CB22 3AT, UK
| | | | | | - Michael Wilson
- Signalling Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Simon Walker
- Imaging Facility, Babraham Institute, Cambridge CB22 3AT, UK
| | | | | | | | - Len R Stephens
- Signalling Programme, Babraham Institute, Cambridge CB22 3AT, UK.
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10
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Sprenger A, Carr HS, Ulu A, Frost JA. Src stimulates Abl-dependent phosphorylation of the guanine exchange factor Net1A to promote its cytosolic localization and cell motility. J Biol Chem 2023; 299:104887. [PMID: 37271338 PMCID: PMC10404680 DOI: 10.1016/j.jbc.2023.104887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 05/26/2023] [Accepted: 05/27/2023] [Indexed: 06/06/2023] Open
Abstract
The neuroepithelial cell transforming gene 1 (Net1) is a guanine nucleotide exchange factor for the small GTPase RhoA that promotes cancer cell motility and metastasis. Two isoforms of Net1 exist, Net1 and Net1A, both of which are sequestered in the nucleus in quiescent cells to prevent aberrant RhoA activation. Many cell motility stimuli drive cytosolic relocalization of Net1A, but mechanisms controlling this event are not fully understood. Here, we demonstrate that epithelial growth factor stimulates protein kinase Src- and Abl1-dependent phosphorylation of Net1A to promote its cytosolic localization. We show that Abl1 efficiently phosphorylates Net1A on Y373, and that phenylalanine substitution of Y373 prevents Net1A cytosolic localization. Furthermore, we found that Abl1-driven cytosolic localization of Net1A does not require S52, which is a phosphorylation site of a different kinase, c-Jun N-terminal kinase, that inhibits nuclear import of Net1A. However, we did find that MKK7-stimulated cytosolic localization of Net1A does require Y373. We also demonstrate that aspartate substitution at Y373 is sufficient to promote Net1A cytosolic accumulation, and expression of Net1A Y373D potentiates epithelial growth factor-stimulated RhoA activation, downstream myosin light chain 2 phosphorylation, and F-actin accumulation. Moreover, we show that expression of Net1A Y373D in breast cancer cells also significantly increases cell motility and Matrigel invasion. Finally, we show that Net1A is required for Abl1-stimulated cell motility, which is rescued by expression of Net1A Y373D, but not Net1A Y373F. Taken together, this work demonstrates a novel mechanism controlling Net1A subcellular localization to regulate RhoA-dependent cell motility and invasion.
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Affiliation(s)
- Ashabari Sprenger
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Heather S Carr
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Arzu Ulu
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Jeffrey A Frost
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas, USA.
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11
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Vieira RC, Pinho LG, Westerberg LS. Understanding immunoactinopathies: A decade of research on WAS gene defects. Pediatr Allergy Immunol 2023; 34:e13951. [PMID: 37102395 DOI: 10.1111/pai.13951] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 04/28/2023]
Abstract
Immunoactinopathies caused by mutations in actin-related proteins are a growing group of inborn errors of immunity (IEI). Immunoactinopathies are caused by a dysregulated actin cytoskeleton and affect hematopoietic cells especially because of their unique capacity to survey the body for invading pathogens and altered self, such as cancer cells. These cell motility and cell-to-cell interaction properties depend on the dynamic nature of the actin cytoskeleton. Wiskott-Aldrich syndrome (WAS) is the archetypical immunoactinopathy and the first described. WAS is caused by loss-of-function and gain-of-function mutations in the actin regulator WASp, uniquely expressed in hematopoietic cells. Mutations in WAS cause a profound disturbance of actin cytoskeleton regulation of hematopoietic cells. Studies during the last 10 years have shed light on the specific effects on different hematopoietic cells, revealing that they are not affected equally by mutations in the WAS gene. Moreover, the mechanistic understanding of how WASp controls nuclear and cytoplasmatic activities may help to find therapeutic alternatives according to the site of the mutation and clinical phenotypes. In this review, we summarize recent findings that have added to the complexity and increased our understanding of WAS-related diseases and immunoactinopathies.
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Affiliation(s)
- Rhaissa Calixto Vieira
- Department of Microbiology, Tumor and Cell biology, Karolinska Institutet, Stockholm, Sweden
| | - Lia Goncalves Pinho
- Department of Microbiology, Tumor and Cell biology, Karolinska Institutet, Stockholm, Sweden
| | - Lisa S Westerberg
- Department of Microbiology, Tumor and Cell biology, Karolinska Institutet, Stockholm, Sweden
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12
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The noncatalytic regions of the tyrosine kinase Tnk1 are important for activity and substrate specificity. J Biol Chem 2022; 298:102664. [PMID: 36334623 DOI: 10.1016/j.jbc.2022.102664] [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: 04/15/2022] [Revised: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 11/29/2022] Open
Abstract
Human Tnk1 (thirty-eight negative kinase 1) is a member of the Ack family of nonreceptor tyrosine kinases. Tnk1 contains a sterile alpha motif, a tyrosine kinase catalytic domain, an SH3 (Src homology 3) domain, and a large C-terminal region that contains a ubiquitin association domain. However, specific physiological roles for Tnk1 have not been characterized in depth. Here, we expressed and purified Tnk1 from Sf9 insect cells and established an in vitro assay system using a peptide substrate derived from the Wiskott-Aldrich Syndrome Protein (WASP). By Tnk1 expression in mammalian cells, we found that the N-terminal SAM domain is important for self-association and kinase activity. We also studied a fusion protein, originally discovered in a Hodgkin's Lymphoma cell line, that contains an unrelated sequence from the C17ORF61 gene fused to the C-terminus of Tnk1. Cells expressing the fusion protein showed increased tyrosine phosphorylation of cellular substrates relative to cells expressing WT Tnk1. A truncated Tnk1 construct (residues 1-465) also showed enhanced phosphorylation, indicating that the C17ORF61 sequence was dispensable for the effect. Additionally, in vitro kinase assays with the WASP peptide substrate showed no increase in intrinsic Tnk1 activity in C-terminally truncated constructs, suggesting that the truncations did not simply remove an autoinhibitory element. Fluorescence microscopy experiments demonstrated that the C-terminus of Tnk1 plays an important role in the subcellular localization of the kinase. Taken together, our data suggest that the noncatalytic regions of Tnk1 play important roles in governing activity and substrate phosphorylation.
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13
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Dickerson MT, Dadi PK, Zaborska KE, Nakhe AY, Schaub CM, Dobson JR, Wright NM, Lynch JC, Scott CF, Robinson LD, Jacobson DA. G i/o protein-coupled receptor inhibition of beta-cell electrical excitability and insulin secretion depends on Na +/K + ATPase activation. Nat Commun 2022; 13:6461. [PMID: 36309517 PMCID: PMC9617941 DOI: 10.1038/s41467-022-34166-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 10/17/2022] [Indexed: 12/25/2022] Open
Abstract
Gi/o-coupled somatostatin or α2-adrenergic receptor activation stimulated β-cell NKA activity, resulting in islet Ca2+ fluctuations. Furthermore, intra-islet paracrine activation of β-cell Gi/o-GPCRs and NKAs by δ-cell somatostatin secretion slowed Ca2+ oscillations, which decreased insulin secretion. β-cell membrane potential hyperpolarization resulting from Gi/o-GPCR activation was dependent on NKA phosphorylation by Src tyrosine kinases. Whereas, β-cell NKA function was inhibited by cAMP-dependent PKA activity. These data reveal that NKA-mediated β-cell membrane potential hyperpolarization is the primary and conserved mechanism for Gi/o-GPCR control of electrical excitability, Ca2+ handling, and insulin secretion.
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Affiliation(s)
- Matthew T Dickerson
- Molecular Physiology and Biophysics Department, Vanderbilt University, 7425B MRB IV, 2213 Garland Ave., Nashville, TN, USA
| | - Prasanna K Dadi
- Molecular Physiology and Biophysics Department, Vanderbilt University, 7425B MRB IV, 2213 Garland Ave., Nashville, TN, USA
| | - Karolina E Zaborska
- Molecular Physiology and Biophysics Department, Vanderbilt University, 7425B MRB IV, 2213 Garland Ave., Nashville, TN, USA
| | - Arya Y Nakhe
- Molecular Physiology and Biophysics Department, Vanderbilt University, 7425B MRB IV, 2213 Garland Ave., Nashville, TN, USA
| | - Charles M Schaub
- Molecular Physiology and Biophysics Department, Vanderbilt University, 7425B MRB IV, 2213 Garland Ave., Nashville, TN, USA
| | - Jordyn R Dobson
- Molecular Physiology and Biophysics Department, Vanderbilt University, 7425B MRB IV, 2213 Garland Ave., Nashville, TN, USA
| | - Nicole M Wright
- Molecular Physiology and Biophysics Department, Vanderbilt University, 7425B MRB IV, 2213 Garland Ave., Nashville, TN, USA
| | - Joshua C Lynch
- Molecular Physiology and Biophysics Department, Vanderbilt University, 7425B MRB IV, 2213 Garland Ave., Nashville, TN, USA
| | - Claire F Scott
- Molecular Physiology and Biophysics Department, Vanderbilt University, 7425B MRB IV, 2213 Garland Ave., Nashville, TN, USA
| | - Logan D Robinson
- Molecular Physiology and Biophysics Department, Vanderbilt University, 7425B MRB IV, 2213 Garland Ave., Nashville, TN, USA
| | - David A Jacobson
- Molecular Physiology and Biophysics Department, Vanderbilt University, 7425B MRB IV, 2213 Garland Ave., Nashville, TN, USA.
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14
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Raman R, Villefranc JA, Ullmann TM, Thiesmeyer J, Anelli V, Yao J, Hurley JR, Pauli C, Bareja R, Wha Eng K, Dorsaint P, Wilkes DC, Beg S, Kudman S, Shaw R, Churchill M, Ahmed A, Keefer L, Misner I, Nichol D, Gumpeni N, Scognamiglio T, Rubin MA, Grandori C, Solomon JP, Song W, Mosquera JM, Dephoure N, Sboner A, Elemento O, Houvras Y. Inhibition of FGF receptor blocks adaptive resistance to RET inhibition in CCDC6-RET-rearranged thyroid cancer. J Exp Med 2022; 219:e20210390. [PMID: 35510953 PMCID: PMC9082625 DOI: 10.1084/jem.20210390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 11/23/2021] [Accepted: 03/18/2022] [Indexed: 11/18/2022] Open
Abstract
Genetic alterations in RET lead to activation of ERK and AKT signaling and are associated with hereditary and sporadic thyroid cancer and lung cancer. Highly selective RET inhibitors have recently entered clinical use after demonstrating efficacy in treating patients with diverse tumor types harboring RET gene rearrangements or activating mutations. In order to understand resistance mechanisms arising after treatment with RET inhibitors, we performed a comprehensive molecular and genomic analysis of a patient with RET-rearranged thyroid cancer. Using a combination of drug screening and proteomic and biochemical profiling, we identified an adaptive resistance to RET inhibitors that reactivates ERK signaling within hours of drug exposure. We found that activation of FGFR signaling is a mechanism of adaptive resistance to RET inhibitors that activates ERK signaling. Combined inhibition of FGFR and RET prevented the development of adaptive resistance to RET inhibitors, reduced cell viability, and decreased tumor growth in cellular and animal models of CCDC6-RET-rearranged thyroid cancer.
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Affiliation(s)
- Renuka Raman
- Department of Surgery, Weill Cornell Medical College, New York, NY
| | | | | | | | - Viviana Anelli
- Department of Surgery, Weill Cornell Medical College, New York, NY
| | - Jun Yao
- Department of Surgery, Weill Cornell Medical College, New York, NY
| | - James R. Hurley
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Chantal Pauli
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Rohan Bareja
- The Caryl and Israel Englander Institute for Precision Medicine and the Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY
| | - Kenneth Wha Eng
- The Caryl and Israel Englander Institute for Precision Medicine and the Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY
| | - Princesca Dorsaint
- The Caryl and Israel Englander Institute for Precision Medicine and the Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY
| | - David C. Wilkes
- The Caryl and Israel Englander Institute for Precision Medicine and the Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY
| | - Shaham Beg
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Sarah Kudman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Reid Shaw
- SEngine Precision Medicine, Seattle, WA
| | | | - Adnan Ahmed
- Department of Biochemistry, Weill Cornell Medical College, New York, NY
| | | | - Ian Misner
- Personal Genome Diagnostics, Inc., Baltimore, MD
| | - Donna Nichol
- Personal Genome Diagnostics, Inc., Baltimore, MD
| | - Naveen Gumpeni
- Department of Radiology, Weill Cornell Medical College, New York, NY
| | - Theresa Scognamiglio
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Mark A. Rubin
- Bern Center for Precision Medicine, University of Bern, Bern, Switzerland
| | | | - James Patrick Solomon
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Wei Song
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Juan Miguel Mosquera
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Noah Dephoure
- Department of Biochemistry, Weill Cornell Medical College, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medical College, New York, NY
| | - Andrea Sboner
- The Caryl and Israel Englander Institute for Precision Medicine and the Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medical College, New York, NY
| | - Olivier Elemento
- The Caryl and Israel Englander Institute for Precision Medicine and the Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medical College, New York, NY
| | - Yariv Houvras
- Department of Surgery, Weill Cornell Medical College, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medical College, New York, NY
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15
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Mingione VR, Foda Z, Paung Y, Philipose H, Rangwala AM, Shan Y, Seeliger MA. Validation of an allosteric binding site of Src kinase identified by unbiased ligand binding simulations. J Mol Biol 2022; 434:167628. [PMID: 35595169 DOI: 10.1016/j.jmb.2022.167628] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/13/2022] [Accepted: 05/04/2022] [Indexed: 10/18/2022]
Abstract
Allostery plays a primary role in regulating protein activity, making it an important mechanism in human disease and drug discovery. Identifying allosteric regulatory sites to explore their biological significance and therapeutic potential is invaluable to drug discovery; however, identification remains a challenge. Allosteric sites are often "cryptic" without clear geometric or chemical features. Since allosteric regulatory sites are often less conserved in protein kinases than the orthosteric ATP binding site, allosteric ligands are commonly more specific than ATP competitive inhibitors. We present a generalizable computational protocol to predict allosteric ligand binding sites based on unbiased ligand binding simulation trajectories. We demonstrate the feasibility of this protocol by revisiting our previously published ligand binding simulations using the first identified viral proto-oncogene, Src kinase, as a model system. The binding paths for kinase inhibitor PP1 uncovered three metastable intermediate states before binding the high-affinity ATP-binding pocket, revealing two previously known allosteric sites and one novel site. Herein, we validate the novel site using a combination of virtual screening and experimental assays to identify a v-type allosteric small-molecule inhibitor that targets this novel site with specificity for Src over closely related kinases. This study provides a proof-of-concept for employing unbiased ligand binding simulations to identify cryptic allosteric binding sites and is widely applicable to other protein-ligand systems.
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Affiliation(s)
- Victoria R Mingione
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Zachariah Foda
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - YiTing Paung
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Hannah Philipose
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Aziz M Rangwala
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yibing Shan
- Antidote Health Foundation for Cure of Cancer, Cambridge, MA 02139, USA.
| | - Markus A Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA.
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16
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Wu K, Peng X, Chen M, Li Y, Tang G, Peng J, Peng Y, Cao X. Recent progress of research on anti‐tumor agents using benzimidazole as the structure unit. Chem Biol Drug Des 2022; 99:736-757. [DOI: 10.1111/cbdd.14022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/10/2022] [Accepted: 01/15/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Kaiyue Wu
- Institute of Pharmacy and Pharmacology Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study College of Pharmacy Hengyang Medical School University of South China Hengyang China
| | - Xiaoyu Peng
- Institute of Pharmacy and Pharmacology Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study College of Pharmacy Hengyang Medical School University of South China Hengyang China
| | - Miaojia Chen
- Department of Pharmacy the first People's Hospital Pingjiang Yueyang Hunan China
| | - Yang Li
- Institute of Pharmacy and Pharmacology Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study College of Pharmacy Hengyang Medical School University of South China Hengyang China
| | - Guotao Tang
- Institute of Pharmacy and Pharmacology Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study College of Pharmacy Hengyang Medical School University of South China Hengyang China
| | - Junmei Peng
- Institute of Pharmacy and Pharmacology Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study College of Pharmacy Hengyang Medical School University of South China Hengyang China
| | - Yuanyuan Peng
- School of Electrical and Automation Engineering East China Jiaotong University Nanchang 330000 China
| | - Xuan Cao
- Institute of Pharmacy and Pharmacology Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study College of Pharmacy Hengyang Medical School University of South China Hengyang China
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17
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Montecchini O, Braidotti S, Franca R, Zudeh G, Boni C, Sorio C, Toffoletti E, Rabusin M, Tommasini A, Decorti G, Stocco G. A Novel ELISA-Based Peptide Biosensor Assay for Screening ABL1 Activity in vitro: A Challenge for Precision Therapy in BCR-ABL1 and BCR-ABL1 Like Leukemias. Front Pharmacol 2021; 12:749361. [PMID: 34867354 PMCID: PMC8640483 DOI: 10.3389/fphar.2021.749361] [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] [Received: 07/29/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
The pathogenic role of the overactivated ABL1 tyrosine kinase (TK) pathway is well recognized in some forms of BCR-ABL1 like acute lymphoblastic leukemia (ALL); TK inhibitors represent a useful therapeutic choice in these patients who respond poorly to conventional chemotherapy. Here we report a novel peptide biosensor (PABL)-ELISA assay to investigate ABL1 activity in four immortalized leukemic cell lines with different genetic background. The PABL sequence comprises an ABL1 tyrosine (Y) phosphorylation site and a targeting sequence that increases the specificity for ABL1; additional peptides (Y-site-mutated (PABL-F) and fully-phosphorylated (PPHOSPHO-ABL) biosensors) were included in the assay. After incubation with whole cell lysates, average PABL phosphorylation was significantly increased (basal vs. PABL phosphorylation: 6.84 ± 1.46% vs. 32.44 ± 3.25%, p-value < 0.0001, two-way ANOVA, Bonferroni post-test, percentages relative to PPHOSPHO-ABL in each cell line). Cell lines expressing ABL1-chimeric proteins (K562, ALL-SIL) presented the higher TK activity on PABL; a lower signal was instead observed for NALM6 and REH (p < 0.001 and p < 0.05 vs. K562, respectively). Phosphorylation was ABL1-mediated, as demonstrated by the specific inhibition of imatinib (p < 0.001 for K562, NALM6, ALL-SIL and p < 0.01 for REH) in contrast to ruxolitinib (JAK2-inhibitor), and occurred on the ABL1 Y-site, as demonstrated by PABL-F whose phosphorylation was comparable to basal levels. In order to validate this novel PABL-ELISA assay on leukemic cells isolated from patient’s bone marrow aspirates, preliminary analysis on blasts derived from an adult affected by chronic myeloid leukaemia (BCR-ABL1 positive) and a child affected by ALL (BCR-ABL1 negative) were performed. Phosphorylation of PABL was specifically inhibited after the incubation of BCR-ABL1 positive cell lysates with imatinib, but not with ruxolitinib. While requiring further optimization and validation in leukemic blasts to be of clinical interest, the PABL-based ELISA assay provides a novel in vitro tool for screening both the aberrant ABL1 activity in BCR-ABL1 like ALL leukemic cells and their potential response to TK inhibitors.
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Affiliation(s)
- Oksana Montecchini
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Stefania Braidotti
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Raffaella Franca
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Giulia Zudeh
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Christian Boni
- Department of Medicine, University of Verona, Verona, Italy
| | - Claudio Sorio
- Department of Medicine, University of Verona, Verona, Italy
| | - Eleonora Toffoletti
- Division of Hematology and Bone Marrow Transplantation, Azienda Ospedaliero-Universitaria, Udine, Italy
| | - Marco Rabusin
- Institute for Maternal and Child Health (I.R.C.C.S) Burlo Garofolo, Trieste, Italy
| | - Alberto Tommasini
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.,Institute for Maternal and Child Health (I.R.C.C.S) Burlo Garofolo, Trieste, Italy
| | - Giuliana Decorti
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.,Institute for Maternal and Child Health (I.R.C.C.S) Burlo Garofolo, Trieste, Italy
| | - Gabriele Stocco
- Department of Life Sciences, University of Trieste, Trieste, Italy
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18
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Development of 2'-aminospiro [pyrano[3,2-c]quinoline]-3'-carbonitrile derivatives as non-ATP competitive Src kinase inhibitors that suppress breast cancer cell migration and proliferation. Bioorg Chem 2021; 116:105344. [PMID: 34598088 DOI: 10.1016/j.bioorg.2021.105344] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/31/2021] [Accepted: 09/07/2021] [Indexed: 02/03/2023]
Abstract
Src kinase activity controls diverse cellular functions, including cell growth, migration, adhesion, and survival. It is de-regulated in several cancers, including breast cancer, where it is highly expressed and phosphorylated. Thus, targeting Src by a small molecule is a feasible strategy for managing different breast cancer types. Several Src kinase inhibitors are available, including the FDA-approved drug (dasatinib). However, they are primarily ATP-competitive inhibitors that have been reported to lack specificity towards Src. We have a long-time interest in discovering protein kinase inhibitors that are non-competitive for ATP. In this project, three groups of 2'-aminospiro[pyrano[3,2-c]quinoline]-3'-carbonitrile derivatives were designed and synthesized, hypothesizing that small molecules with a spiro scaffold appended to a pyrano[3,2-c]quinoline analog could act as non-ATP competitive Src kinase inhibitors. 3b, 3c, and 3d inhibited Src kinase activity with IC50s of 4.9, 5.9, and 0.9 μM, respectively. At the same time, they did not impact the MDM2/p53 interaction in HEK293 cells, which has been reported to be affected by some spirocyclic compounds. 25 µM of 3b, 3c, or 3d did not inhibit the kinase activity of ERK2, JNK1, or p38-alpha in an in-vitro kinase assay. Steady-state kinetic studies for the effect of 3d on the ability of recombinant Src to phosphorylate its substrate (Srctide) revealed a non-ATP competitive inhibition mechanism. 1.6 µM of 3d was enough to diminish Src, Fak, and paxillin phosphorylation in the breast cancer cell lines MDA-MB-231 and MCF7. In the NCI screening, 3d induced broad tumor cytotoxicity for the NCI-60 cell lines, including all the breast cancer cell lines. The potency of 3b, 3c, and 3d to inhibit migration, proliferation, and colony formation of MDA-MB-231 and proliferation of MCF7 cells correlates with their potency to suppress Src kinase activity in the same cell line. Noticeably, the cell growth suppression and apoptosis induction in the tested cell lines can be attributed to the ability of the new derivatives to suppress the ERK and Akt survival pathways downstream of Src.
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19
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Liu L, Limsakul P, Meng X, Huang Y, Harrison RES, Huang TS, Shi Y, Yu Y, Charupanit K, Zhong S, Lu S, Zhang J, Chien S, Sun J, Wang Y. Integration of FRET and sequencing to engineer kinase biosensors from mammalian cell libraries. Nat Commun 2021; 12:5031. [PMID: 34413312 PMCID: PMC8376904 DOI: 10.1038/s41467-021-25323-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/30/2021] [Indexed: 01/01/2023] Open
Abstract
The limited sensitivity of Förster Resonance Energy Transfer (FRET) biosensors hinders their broader applications. Here, we develop an approach integrating high-throughput FRET sorting and next-generation sequencing (FRET-Seq) to identify sensitive biosensors with varying substrate sequences from large-scale libraries directly in mammalian cells, utilizing the design of self-activating FRET (saFRET) biosensor. The resulting biosensors of Fyn and ZAP70 kinases exhibit enhanced performance and enable the dynamic imaging of T-cell activation mediated by T cell receptor (TCR) or chimeric antigen receptor (CAR), revealing a highly organized ZAP70 subcellular activity pattern upon TCR but not CAR engagement. The ZAP70 biosensor elucidates the role of immunoreceptor tyrosine-based activation motif (ITAM) in affecting ZAP70 activation to regulate CAR functions. A saFRET biosensor-based high-throughput drug screening (saFRET-HTDS) assay further enables the identification of an FDA-approved cancer drug, Sunitinib, that can be repurposed to inhibit ZAP70 activity and autoimmune-disease-related T-cell activation.
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Affiliation(s)
- Longwei Liu
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
| | - Praopim Limsakul
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
- Center of Excellence for Trace Analysis and Biosensor, Division of Physical Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Xianhui Meng
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, P.R. China
| | - Yan Huang
- Department of Chemistry and Chemical Engineering, Hunan University, Changsha, P.R. China
| | - Reed E S Harrison
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
| | - Tse-Shun Huang
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
- BioLegend, San Diego, CA, USA
| | - Yiwen Shi
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
| | - Yiyan Yu
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
| | - Krit Charupanit
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Sheng Zhong
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
| | - Shaoying Lu
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, CA, USA
| | - Shu Chien
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA
- Department of Medicine, University of California, San Diego, CA, USA
| | - Jie Sun
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, P.R. China.
| | - Yingxiao Wang
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, USA.
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20
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Tapia L, Solozabal N, Solà J, Pérez Y, Miller WT, Alfonso I. Modulation of Src Kinase Activity by Selective Substrate Recognition with Pseudopeptidic Cages. Chemistry 2021; 27:9542-9549. [PMID: 33904620 PMCID: PMC8362067 DOI: 10.1002/chem.202100990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Indexed: 12/15/2022]
Abstract
The selective recognition of tyrosine residues in peptides is an appealing approach to inhibiting their tyrosine kinase (TK)-mediated phosphorylation. Herein, we describe pseudopeptidic cages that efficiently protect substrates from the action of the Src TK enzyme, precluding the corresponding Tyr phosphorylation. Fluorescence emission titrations show that the most efficient cage inhibitors strongly bind the peptide substrates with a very good correlation between the binding constant and the inhibitory potency. Structural insights and additional control experiments further support the proposed mechanism of selective supramolecular protection of the substrates. Moreover, the approach also works in a completely different kinase-substrate system. These results illustrate the potential of supramolecular complexes for the efficient and selective modulation of TK signaling.
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Affiliation(s)
- Lucía Tapia
- Department of Biological ChemistryInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - Naiara Solozabal
- NMR FacilityInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - Jordi Solà
- Department of Biological ChemistryInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - Yolanda Pérez
- NMR FacilityInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - W. Todd Miller
- Department of Physiology and BiophysicsStony Brook University and Department of Veterans Affairs Medical CenterStony BrookNY, 11794USA
| | - Ignacio Alfonso
- Department of Biological ChemistryInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
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21
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Receptor tyrosine kinases and cancer: oncogenic mechanisms and therapeutic approaches. Oncogene 2021; 40:4079-4093. [PMID: 34079087 DOI: 10.1038/s41388-021-01841-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/29/2021] [Accepted: 05/13/2021] [Indexed: 02/05/2023]
Abstract
Receptor tyrosine kinases (RTKs) are transmembrane receptors of great clinical interest due to their role in disease, notably cancer. Since their discovery, several mechanisms of RTK dysregulation have been identified, resulting in multiple cancer types displaying 'oncogenic addiction' to RTKs. As a result, RTKs have represented a major class for targeted therapeutics over the past two decades, with numerous small molecule-based tyrosine kinase inhibitor (TKI) therapeutics having been developed and clinically approved for several cancers. However, many of the current RTK inhibitor treatments eventually result in the rapid development of acquired resistance and subsequent tumor relapse. Recent technological advances and tools are being generated for the identification of novel RTK small molecule therapeutics. These newer technologies will be important for the identification of diverse types of RTK inhibitors, targeting both the receptors themselves as well as key cellular factors that play important roles in the RTK signaling cascade.
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22
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An assay of human tyrosine protein kinase ABL activity using an Escherichia coli protein expression system. Biotechniques 2021; 70:209-217. [PMID: 33820471 DOI: 10.2144/btn-2020-0154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
ABL, a human tyrosine protein kinase, and its substrate are co-expressed in Escherichia coli. Tyrosine phosphorylation of the substrate in E. coli was detected using Phos-tag SDS-PAGE. The bacterial co-expression system was used as a field for the kinase reaction to evaluate the enzymatic activity of five types of ABL kinase domain mutants. Relative to wild-type ABL, kinase activity was comparable in the H396P mutant, reduced in both Y253F and E255K mutants and undetectable in T315I and M351T mutants. These comparative results demonstrated that the phosphorylation states of the mutants correlated with their activity. The bacterial co-expression system permits rapid production of tyrosine kinase variants and provides a simple approach for examining their structure-activity relationships.
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23
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Carabias A, Gómez-Hernández M, de Cima S, Rodríguez-Blázquez A, Morán-Vaquero A, González-Sáenz P, Guerrero C, de Pereda JM. Mechanisms of autoregulation of C3G, activator of the GTPase Rap1, and its catalytic deregulation in lymphomas. Sci Signal 2020; 13:13/647/eabb7075. [PMID: 32873726 DOI: 10.1126/scisignal.abb7075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
C3G is a guanine nucleotide exchange factor (GEF) that regulates cell adhesion and migration by activating the GTPase Rap1. The GEF activity of C3G is stimulated by the adaptor proteins Crk and CrkL and by tyrosine phosphorylation. Here, we uncovered mechanisms of C3G autoinhibition and activation. Specifically, we found that two intramolecular interactions regulate the activity of C3G. First, an autoinhibitory region (AIR) within the central domain of C3G binds to and blocks the catalytic Cdc25H domain. Second, the binding of the protein's N-terminal domain to its Ras exchanger motif (REM) is required for its GEF activity. CrkL activated C3G by displacing the AIR/Cdc25HD interaction. Two missense mutations in the AIR found in non-Hodgkin's lymphomas, Y554H and M555K, disrupted the autoinhibitory mechanism. Expression of C3G-Y554H or C3G-M555K in Ba/F3 pro-B cells caused constitutive activation of Rap1 and, consequently, the integrin LFA-1. Our findings suggest that sustained Rap1 activation by deregulated C3G might promote progression of lymphomas and that designing therapeutics to target C3G might treat these malignancies.
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Affiliation(s)
- Arturo Carabias
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, 37007 Salamanca, Spain
| | - María Gómez-Hernández
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, 37007 Salamanca, Spain
| | - Sergio de Cima
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, 37007 Salamanca, Spain
| | - Antonio Rodríguez-Blázquez
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, 37007 Salamanca, Spain
| | - Alba Morán-Vaquero
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, 37007 Salamanca, Spain
| | - Patricia González-Sáenz
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, 37007 Salamanca, Spain
| | - Carmen Guerrero
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, 37007 Salamanca, Spain.,Departamento de Medicina, Facultad de Medicina, Universidad de Salamanca, Instituto de Investigación Biomédica de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - José M de Pereda
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, 37007 Salamanca, Spain.
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24
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Radiochemical and biological properties of peptides designed to interact with EGF receptor: Relevance for glioblastoma. Nucl Med Biol 2020; 88-89:14-23. [PMID: 32663774 DOI: 10.1016/j.nucmedbio.2020.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/20/2020] [Accepted: 07/02/2020] [Indexed: 01/04/2023]
Abstract
Radiolabeled peptides with high specificity to receptors expressed on tumor cells hold a great promise as diagnostic and therapeutic tracers. The main objective of this study was to evaluate the radiochemical and biological properties of two [131I]I-peptides, as well as their interaction with the epidermal growth factor receptor (EGFR), overexpressed in a wide variety of tumors, including glioblastoma. The EEEEYFELV peptide and its analogue DEDEYFELV, both designed to interact with EGFR, were chemically synthesized, purified and radiolabeled with iodine-131 ([131I]NaI). The radioiodination was evaluated and optimized using the chloramine-T methodology. The stability, serum proteins binding and partition coefficient were assessed for both radioconjugates. Moreover, the binding and internalization of synthesized radiopeptides with rat glioblastoma cells (C6) and with rat brain homogenates from a glioblastoma induced model were evaluated and ex vivo biodistribution studies were performed. Under optimized radiolabeling conditions, the peptides showed an average radiochemical yield of 90-95%. The stability studies showed that both peptides were stable up to 24 h in reaction medium, saline, and human serum. Furthermore, [131I]I-peptides have hydrophilic features and showed binding percentage to serum proteins of around 50%, which is highly compatible with clinical applications. Moreover, the radiopeptides presented capacity for binding and internalization in both tumor cells (C6) and rat brain tissues after tumor induction. Biodistribution studies corroborated the cell culture studies and confirmed the different binding characteristics derived from a simple change of two amino acids (Glu ➔ Asp1,3) in their sequences. The results obtained are consistent enough to motivate further studies. Thereby, these radiolabeled peptides might be useful for diagnostic applications.
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25
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Washington C, Chernet R, Gokhale RH, Martino-Cortez Y, Liu HY, Rosenberg AM, Shahar S, Pfleger CM. A conserved, N-terminal tyrosine signal directs Ras for inhibition by Rabex-5. PLoS Genet 2020; 16:e1008715. [PMID: 32559233 PMCID: PMC7329146 DOI: 10.1371/journal.pgen.1008715] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 07/01/2020] [Accepted: 03/13/2020] [Indexed: 01/08/2023] Open
Abstract
Dysregulation of the Ras oncogene in development causes developmental disorders, "Rasopathies," whereas mutational activation or amplification of Ras in differentiated tissues causes cancer. Rabex-5 (also called RabGEF1) inhibits Ras by promoting Ras mono- and di-ubiquitination. We report here that Rabex-5-mediated Ras ubiquitination requires Ras Tyrosine 4 (Y4), a site of known phosphorylation. Ras substitution mutants insensitive to Y4 phosphorylation did not undergo Rabex-5-mediated ubiquitination in cells and exhibited Ras gain-of-function phenotypes in vivo. Ras Y4 phosphomimic substitution increased Rabex-5-mediated ubiquitination in cells. Y4 phosphomimic substitution in oncogenic Ras blocked the morphological phenotypes associated with oncogenic Ras in vivo dependent on the presence of Rabex-5. We developed polyclonal antibodies raised against an N-terminal Ras peptide phosphorylated at Y4. These anti-phospho-Y4 antibodies showed dramatic recognition of recombinant wild-type Ras and RasG12V proteins when incubated with JAK2 or SRC kinases but not of RasY4F or RasY4F,G12V recombinant proteins suggesting that JAK2 and SRC could promote phosphorylation of Ras proteins at Y4 in vitro. Anti-phospho-Y4 antibodies also showed recognition of RasG12V protein, but not wild-type Ras, when incubated with EGFR. A role for JAK2, SRC, and EGFR (kinases with well-known roles to activate signaling through Ras), to promote Ras Y4 phosphorylation could represent a feedback mechanism to limit Ras activation and thus establish Ras homeostasis. Notably, rare variants of Ras at Y4 have been found in cerebellar glioblastomas. Therefore, our work identifies a physiologically relevant Ras ubiquitination signal and highlights a requirement for Y4 for Ras inhibition by Rabex-5 to maintain Ras pathway homeostasis and to prevent tissue transformation.
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Affiliation(s)
- Chalita Washington
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Rachel Chernet
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Rewatee H. Gokhale
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Graduate School of Biomedical Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Yesenia Martino-Cortez
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Hsiu-Yu Liu
- Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Ashley M. Rosenberg
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Columbia University, New York, New York, United States of America
| | - Sivan Shahar
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- New York Medical College, Valhalla, New York, United States of America
| | - Cathie M. Pfleger
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Graduate School of Biomedical Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
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26
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Chen L, Marsiglia WM, Chen H, Katigbak J, Erdjument-Bromage H, Kemble DJ, Fu L, Ma J, Sun G, Zhang Y, Liang G, Neubert TA, Li X, Traaseth NJ, Mohammadi M. Molecular basis for receptor tyrosine kinase A-loop tyrosine transphosphorylation. Nat Chem Biol 2020; 16:267-277. [PMID: 31959966 PMCID: PMC7040854 DOI: 10.1038/s41589-019-0455-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 12/05/2019] [Accepted: 12/13/2019] [Indexed: 12/11/2022]
Abstract
A long-standing mystery shrouds the mechanism by which catalytically repressed receptor tyrosine kinase domains accomplish transphosphorylation of activation loop (A-loop) tyrosines. Here we show that this reaction proceeds via an asymmetric complex that is thermodynamically disadvantaged because of an electrostatic repulsion between enzyme and substrate kinases. Under physiological conditions, the energetic gain resulting from ligand-induced dimerization of extracellular domains overcomes this opposing clash, stabilizing the A-loop-transphosphorylating dimer. A unique pathogenic fibroblast growth factor receptor gain-of-function mutation promotes formation of the complex responsible for phosphorylation of A-loop tyrosines by eliminating this repulsive force. We show that asymmetric complex formation induces a more phosphorylatable A-loop conformation in the substrate kinase, which in turn promotes the active state of the enzyme kinase. This explains how quantitative differences in the stability of ligand-induced extracellular dimerization promotes formation of the intracellular A-loop-transphosphorylating asymmetric complex to varying extents, thereby modulating intracellular kinase activity and signaling intensity.
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MESH Headings
- AAA Domain/genetics
- AAA Domain/physiology
- Catalytic Domain
- Dimerization
- Enzyme Activation
- Humans
- Ligands
- Phosphorylation
- Protein Binding
- Protein Conformation
- Protein-Tyrosine Kinases/metabolism
- Protein-Tyrosine Kinases/physiology
- Receptor Protein-Tyrosine Kinases/genetics
- Receptor Protein-Tyrosine Kinases/metabolism
- Receptor Protein-Tyrosine Kinases/physiology
- Receptor, Fibroblast Growth Factor, Type 1/genetics
- Receptor, Fibroblast Growth Factor, Type 1/metabolism
- Receptor, Fibroblast Growth Factor, Type 2/genetics
- Receptor, Fibroblast Growth Factor, Type 2/metabolism
- Receptor, Fibroblast Growth Factor, Type 3/genetics
- Receptor, Fibroblast Growth Factor, Type 3/metabolism
- Signal Transduction
- Structure-Activity Relationship
- Tyrosine/chemistry
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Affiliation(s)
- Lingfeng Chen
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, China
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | | | - Huaibin Chen
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Joseph Katigbak
- Department of Chemistry, New York University, New York, NY, USA
| | - Hediye Erdjument-Bromage
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - David J Kemble
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI, USA
| | - Lili Fu
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jinghong Ma
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Gongqin Sun
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI, USA
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY, USA
| | - Guang Liang
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Thomas A Neubert
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Xiaokun Li
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | | | - Moosa Mohammadi
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
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27
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Smolko CM, Janes KA. An ultrasensitive fiveplex activity assay for cellular kinases. Sci Rep 2019; 9:19409. [PMID: 31857650 PMCID: PMC6923413 DOI: 10.1038/s41598-019-55998-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/30/2019] [Indexed: 02/06/2023] Open
Abstract
Protein kinases are enzymes whose abundance, protein-protein interactions, and posttranslational modifications together determine net signaling activity in cells. Large-scale data on cellular kinase activity are limited, because existing assays are cumbersome, poorly sensitive, low throughput, and restricted to measuring one kinase at a time. Here, we surmount the conventional hurdles of activity measurement with a multiplexing approach that leverages the selectivity of individual kinase-substrate pairs. We demonstrate proof of concept by designing an assay that jointly measures activity of five pleiotropic signaling kinases: Akt, IκB kinase (IKK), c-jun N-terminal kinase (JNK), mitogen-activated protein kinase (MAPK)-extracellular regulated kinase kinase (MEK), and MAPK-activated protein kinase-2 (MK2). The assay operates in a 96-well format and specifically measures endogenous kinase activation with coefficients of variation less than 20%. Multiplex tracking of kinase-substrate pairs reduces input requirements by 25-fold, with ~75 µg of cellular extract sufficient for fiveplex activity profiling. We applied the assay to monitor kinase signaling during coxsackievirus B3 infection of two different host-cell types and identified multiple differences in pathway dynamics and coordination that warrant future study. Because the Akt–IKK–JNK–MEK–MK2 pathways regulate many important cellular functions, the fiveplex assay should find applications in inflammation, environmental-stress, and cancer research.
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Affiliation(s)
- Christian M Smolko
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA
| | - Kevin A Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA. .,Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA.
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28
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Joshi MK, Burton RA, Wu H, Lipchik AM, Craddock BP, Mo H, Parker LL, Miller WT, Post CB. Substrate binding to Src: A new perspective on tyrosine kinase substrate recognition from NMR and molecular dynamics. Protein Sci 2019; 29:350-359. [PMID: 31697410 DOI: 10.1002/pro.3777] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 01/01/2023]
Abstract
Most signal transduction pathways in humans are regulated by protein kinases through phosphorylation of their protein substrates. Typical eukaryotic protein kinases are of two major types: those that phosphorylate-specific sequences containing tyrosine (~90 kinases) and those that phosphorylate either serine or threonine (~395 kinases). The highly conserved catalytic domain of protein kinases comprises a smaller N lobe and a larger C lobe separated by a cleft region lined by the activation loop. Prior studies find that protein tyrosine kinases recognize peptide substrates by binding the polypeptide chain along the C-lobe on one side of the activation loop, while serine/threonine kinases bind their substrates in the cleft and on the side of the activation loop opposite to that of the tyrosine kinases. Substrate binding structural studies have been limited to four families of the tyrosine kinase group, and did not include Src tyrosine kinases. We examined peptide-substrate binding to Src using paramagnetic-relaxation-enhancement NMR combined with molecular dynamics simulations. The results suggest Src tyrosine kinase can bind substrate positioning residues C-terminal to the phosphoacceptor residue in an orientation similar to serine/threonine kinases, and unlike other tyrosine kinases. Mutagenesis corroborates this new perspective on tyrosine kinase substrate recognition. Rather than an evolutionary split between tyrosine and serine/threonine kinases, a change in substrate recognition may have occurred within the TK group of the human kinome. Protein tyrosine kinases have long been therapeutic targets, but many marketed drugs have deleterious off-target effects. More accurate knowledge of substrate interactions of tyrosine kinases has the potential for improving drug selectivity.
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Affiliation(s)
- Mehul K Joshi
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - Robert A Burton
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana.,Ancestry, Lehi, Utah
| | - Heng Wu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - Andrew M Lipchik
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - Barbara P Craddock
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York
| | - Huaping Mo
- Purdue Interdepartmental NMR Facility PINMRF, Purdue University, West Lafayette, Indiana
| | - Laurie L Parker
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - W Todd Miller
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York.,Department of Veterans Affairs Medical Center, Northport, New York
| | - Carol Beth Post
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
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29
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Valgardson J, Cosbey R, Houser P, Rupp M, Van Bronkhorst R, Lee M, Jagodzinski F, Amacher JF. MotifAnalyzer-PDZ: A computational program to investigate the evolution of PDZ-binding target specificity. Protein Sci 2019; 28:2127-2143. [PMID: 31599029 DOI: 10.1002/pro.3741] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 12/15/2022]
Abstract
Recognition of short linear motifs (SLiMs) or peptides by proteins is an important component of many cellular processes. However, due to limited and degenerate binding motifs, prediction of cellular targets is challenging. In addition, many of these interactions are transient and of relatively low affinity. Here, we focus on one of the largest families of SLiM-binding domains in the human proteome, the PDZ domain. These domains bind the extreme C-terminus of target proteins, and are involved in many signaling and trafficking pathways. To predict endogenous targets of PDZ domains, we developed MotifAnalyzer-PDZ, a program that filters and compares all motif-satisfying sequences in any publicly available proteome. This approach enables us to determine possible PDZ binding targets in humans and other organisms. Using this program, we predicted and biochemically tested novel human PDZ targets by looking for strong sequence conservation in evolution. We also identified three C-terminal sequences in choanoflagellates that bind a choanoflagellate PDZ domain, the Monsiga brevicollis SHANK1 PDZ domain (mbSHANK1), with endogenously-relevant affinities, despite a lack of conservation with the targets of a homologous human PDZ domain, SHANK1. All three are predicted to be signaling proteins, with strong sequence homology to cytosolic and receptor tyrosine kinases. Finally, we analyzed and compared the positional amino acid enrichments in PDZ motif-satisfying sequences from over a dozen organisms. Overall, MotifAnalyzer-PDZ is a versatile program to investigate potential PDZ interactions. This proof-of-concept work is poised to enable similar types of analyses for other SLiM-binding domains (e.g., MotifAnalyzer-Kinase). MotifAnalyzer-PDZ is available at http://motifAnalyzerPDZ.cs.wwu.edu.
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Affiliation(s)
- Jordan Valgardson
- Department of Computer Science, Western Washington University, Bellingham, Washington.,Department of Chemistry, Western Washington University, Bellingham, Washington
| | - Robin Cosbey
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Paul Houser
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Milo Rupp
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Raiden Van Bronkhorst
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Michael Lee
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Filip Jagodzinski
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Jeanine F Amacher
- Department of Chemistry, Western Washington University, Bellingham, Washington
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30
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Li B, He J, Lv H, Liu Y, Lv X, Zhang C, Zhu Y, Ai D. c-Abl regulates YAPY357 phosphorylation to activate endothelial atherogenic responses to disturbed flow. J Clin Invest 2019; 129:1167-1179. [PMID: 30629551 DOI: 10.1172/jci122440] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 01/03/2019] [Indexed: 12/26/2022] Open
Abstract
Local flow patterns determine the uneven distribution of atherosclerotic lesions. This research aims to elucidate the mechanism of regulation of nuclear translocation of Yes-associated protein (YAP) under oscillatory shear stress (OSS) in the atheroprone phenotype of endothelial cells (ECs). We report here that OSS led to tyrosine phosphorylation and strong, continuous nuclear translocation of YAP in ECs that is dependent on integrin α5β1 activation. YAP overexpression in ECs blunted the anti-atheroprone effect of an integrin α5β1-blocking peptide (ATN161) in Apoe-/- mice. Activation of integrin α5β1 induced tyrosine, but not serine, phosphorylation of YAP in ECs. Blockage of integrin α5β1 with ATN161 abolished the phosphorylation of YAP at Y357 induced by OSS. Mechanistic studies showed that c-Abl inhibitor attenuated the integrin α5β1-induced YAP tyrosine phosphorylation. Furthermore, the phosphorylation of c-Abl and YAPY357 was significantly increased in ECs in atherosclerotic vessels of mice and in human plaques versus normal vessels. Finally, bosutinib, a tyrosine kinase inhibitor, markedly reduced the level of YAPY357 and the development of atherosclerosis in Apoe-/- mice. The c-Abl/YAPY357 pathway serves as a mechanism for the activation of integrin α5β1 and the atherogenic phenotype of ECs in response to OSS, and provides a potential therapeutic strategy for atherogenesis.
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31
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Ma X, Zhang L, Song J, Nguyen E, Lee RS, Rodgers SJ, Li F, Huang C, Schittenhelm RB, Chan H, Chheang C, Wu J, Brown KK, Mitchell CA, Simpson KJ, Daly RJ. Characterization of the Src-regulated kinome identifies SGK1 as a key mediator of Src-induced transformation. Nat Commun 2019; 10:296. [PMID: 30655532 PMCID: PMC6336867 DOI: 10.1038/s41467-018-08154-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 12/20/2018] [Indexed: 12/13/2022] Open
Abstract
Despite significant progress, our understanding of how specific oncogenes transform cells is still limited and likely underestimates the complexity of downstream signalling events. To address this gap, we use mass spectrometry-based chemical proteomics to characterize the global impact of an oncogene on the expressed kinome, and then functionally annotate the regulated kinases. As an example, we identify 63 protein kinases exhibiting altered expression and/or phosphorylation in Src-transformed mammary epithelial cells. An integrated siRNA screen identifies nine kinases, including SGK1, as being essential for Src-induced transformation. Accordingly, we find that Src positively regulates SGK1 expression in triple negative breast cancer cells, which exhibit a prominent signalling network governed by Src family kinases. Furthermore, combined inhibition of Src and SGK1 reduces colony formation and xenograft growth more effectively than either treatment alone. Therefore, this approach not only provides mechanistic insights into oncogenic transformation but also aids the design of improved therapeutic strategies. The systemic understanding of oncogenic kinase signalling is still limited. Here, the authors combine chemical proteomics with functional screens to assess the impact of oncogenic Src on the expressed kinome and identify SGK1 as a critical mediator of Src-induced cell transformation.
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Affiliation(s)
- Xiuquan Ma
- Cancer Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Luxi Zhang
- Cancer Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Jiangning Song
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia.,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia.,Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC, 3800, Australia
| | - Elizabeth Nguyen
- Cancer Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Rachel S Lee
- Cancer Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Samuel J Rodgers
- Cancer Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Fuyi Li
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia.,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
| | - Cheng Huang
- Monash Biomedical Proteomics Facility and Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
| | - Ralf B Schittenhelm
- Monash Biomedical Proteomics Facility and Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
| | - Howard Chan
- Cancer Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Chanly Chheang
- Cancer Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Jianmin Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Centre for Cancer Bioinformatics, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Kristin K Brown
- Cancer Therapeutics Program and Cancer Metabolism Program, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.,Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC, 3010, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Christina A Mitchell
- Cancer Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Kaylene J Simpson
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, 3010, Australia.,Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Roger J Daly
- Cancer Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia. .,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia.
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32
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Li L, Cui Y, Shen J, Dobson H, Sun G. Evidence for activated Lck protein tyrosine kinase as the driver of proliferation in acute myeloid leukemia cell, CTV-1. Leuk Res 2019; 78:12-20. [PMID: 30660961 DOI: 10.1016/j.leukres.2019.01.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 01/12/2019] [Accepted: 01/14/2019] [Indexed: 01/19/2023]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous group of fast growing cancers of myeloid progenitor cells, for which effective treatments are still lacking. Identification of signaling inhibitors that block their proliferation could reveal the proliferative mechanism of a given leukemia cell, and provide small molecule drugs for targeted therapy for AML. In this study, kinase inhibitors that block the majority of cancer signaling pathways are evaluated for their inhibition of two AML cell lines of the M5 subtypes, CTV-1 and THP-1. While THP-1 cells do not respond to any of these inhibitors, CTV-1 cells are potently inhibited by dasatinib, bosutinib, crizotinib, A-770041, and WH-4-23, all potent inhibitors for Lck, a Src family kinase. CTV-1 cells contain a kinase activity that phosphorylates an Lck-specific peptide substrate in an Lck inhibitor-sensitive manner. Furthermore, the Lck gene is over-expressed in CTV-1, and it contains four mutations, two of which are located in regions critical for Lck negative regulation, and are confirmed to activate Lck. Collectively, these results provide strong evidence that mutated and overexpressed Lck is driving CTV-1 proliferation. While Lck activation and overexpression is rare in AML, this study provides a potential therapeutic strategy for treating patients with a similar oncogenic mechanism.
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Affiliation(s)
- Li Li
- Department of Cell Biology and Medical Genetics, School of Basic Medical Science, Shanxi Medical University, Taiyuan, Shanxi, China; Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI, USA
| | - Yixin Cui
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI, USA
| | - Jinyan Shen
- Department of Cell Biology and Medical Genetics, School of Basic Medical Science, Shanxi Medical University, Taiyuan, Shanxi, China; Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI, USA
| | - Hannah Dobson
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI, USA
| | - Gongqin Sun
- Department of Cell Biology and Medical Genetics, School of Basic Medical Science, Shanxi Medical University, Taiyuan, Shanxi, China; Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI, USA.
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Proctor A, Wang Q, Lawrence DS, Allbritton NL. Selection and optimization of enzyme reporters for chemical cytometry. Methods Enzymol 2019; 622:221-248. [PMID: 31155054 PMCID: PMC6905852 DOI: 10.1016/bs.mie.2019.02.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Chemical cytometry, sensitive analytical measurements of single cells, reveals inherent heterogeneity of cells within a population which is masked or averaged out when using bulk analysis techniques. A particular challenge of chemical cytometry is the development of a suitable reporter or probe for the desired measurement. These reporters must be sufficiently specific for measuring the desired process; possess a lifetime long enough to accomplish the measurement; and have the ability to be loaded into single cells. This chapter details our approach to rationally design and improve peptide substrates as reporters of enzyme activity utilizing chemical cytometry. This method details the iterative approach used to design, characterize, and identify a peptidase-resistant peptide reporter which acts as a kinase substrate within intact cells. Small-scale, rationally designed peptide libraries are generated to rapidly and economically screen candidate reporter peptides for substrate suitability and peptidase resistance. Also detailed are strategies to characterize and validate the designed reporters by determining kinetic parameters, intracellular substrate specificity, resistance to degradation by intracellular peptidases, and behavior within lysates and intact cells.
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Affiliation(s)
- Angela Proctor
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, United States
| | - Qunzhao Wang
- Department of Chemical Biology and Medicinal Chemistry, School of Pharmacy, University of North Carolina, Chapel Hill, NC, United States
| | - David S Lawrence
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, United States; Department of Chemical Biology and Medicinal Chemistry, School of Pharmacy, University of North Carolina, Chapel Hill, NC, United States
| | - Nancy L Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, United States; Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill; North Carolina State University, Raleigh, NC, United States.
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34
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Understanding molecular mechanisms in cell signaling through natural and artificial sequence variation. Nat Struct Mol Biol 2018; 26:25-34. [PMID: 30598552 DOI: 10.1038/s41594-018-0175-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 11/16/2018] [Indexed: 02/08/2023]
Abstract
The functionally tolerated sequence space of proteins can now be explored in an unprecedented way, owing to the expansion of genomic databases and the development of high-throughput methods to interrogate protein function. For signaling proteins, several recent studies have shown how the analysis of sequence variation leverages the available protein-structure information to provide new insights into specificity and allosteric regulation. In this Review, we discuss recent work that illustrates how this emerging approach is providing a deeper understanding of signaling proteins.
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35
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Campbell H, Heidema C, Pilarczyk DG, DeMali KA. SHP-2 is activated in response to force on E-cadherin and dephosphorylates vinculin Y822. J Cell Sci 2018; 131:jcs.216648. [PMID: 30478196 DOI: 10.1242/jcs.216648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 11/16/2018] [Indexed: 11/20/2022] Open
Abstract
The response of cells to mechanical inputs is a key determinant of cell behavior. In response to external forces, E-cadherin initiates signal transduction cascades that allow the cell to modulate its contractility to withstand the force. Much attention has focused on identifying the E-cadherin signaling pathways that promote contractility, but the negative regulators remain undefined. In this study, we identify SHP-2 as a force-activated phosphatase that negatively regulates E-cadherin force transmission by dephosphorylating vinculin Y822. To specifically probe a role for SHP-2 in E-cadherin mechanotransduction, we mutated vinculin so that it retains its phosphorylation but cannot be dephosphorylated. Cells expressing the mutant vinculin have increased contractility. This work provides a mechanism for inactivating E-cadherin mechanotransduction and provides a new method for specifically targeting the action of phosphatases in cells.
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Affiliation(s)
- Hannah Campbell
- Department of Biochemistry and the Interdisciplinary Program in Molecular and Cellular Biology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Christy Heidema
- Department of Biochemistry and the Interdisciplinary Program in Molecular and Cellular Biology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Daisy G Pilarczyk
- Department of Biochemistry and the Interdisciplinary Program in Molecular and Cellular Biology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Kris A DeMali
- Department of Biochemistry and the Interdisciplinary Program in Molecular and Cellular Biology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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36
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Shah NH, Amacher JF, Nocka LM, Kuriyan J. The Src module: an ancient scaffold in the evolution of cytoplasmic tyrosine kinases. Crit Rev Biochem Mol Biol 2018; 53:535-563. [PMID: 30183386 PMCID: PMC6328253 DOI: 10.1080/10409238.2018.1495173] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Tyrosine kinases were first discovered as the protein products of viral oncogenes. We now know that this large family of metazoan enzymes includes nearly one hundred structurally diverse members. Tyrosine kinases are broadly classified into two groups: the transmembrane receptor tyrosine kinases, which sense extracellular stimuli, and the cytoplasmic tyrosine kinases, which contain modular ligand-binding domains and propagate intracellular signals. Several families of cytoplasmic tyrosine kinases have in common a core architecture, the "Src module," composed of a Src-homology 3 (SH3) domain, a Src-homology 2 (SH2) domain, and a kinase domain. Each of these families is defined by additional elaborations on this core architecture. Structural, functional, and evolutionary studies have revealed a unifying set of principles underlying the activity and regulation of tyrosine kinases built on the Src module. The discovery of these conserved properties has shaped our knowledge of the workings of protein kinases in general, and it has had important implications for our understanding of kinase dysregulation in disease and the development of effective kinase-targeted therapies.
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Affiliation(s)
- Neel H. Shah
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Jeanine F. Amacher
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Laura M. Nocka
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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37
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Creixell P, Pandey JP, Palmeri A, Bhattacharyya M, Creixell M, Ranganathan R, Pincus D, Yaffe MB. Hierarchical Organization Endows the Kinase Domain with Regulatory Plasticity. Cell Syst 2018; 7:371-383.e4. [PMID: 30243563 DOI: 10.1016/j.cels.2018.08.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 06/24/2018] [Accepted: 08/13/2018] [Indexed: 02/08/2023]
Abstract
The functional diversity of kinases enables specificity in cellular signal transduction. Yet how more than 500 members of the human kinome specifically receive regulatory inputs and convey information to appropriate substrates-all while using the common signaling output of phosphorylation-remains enigmatic. Here, we perform statistical co-evolution analysis, mutational scanning, and quantitative live-cell assays to reveal a hierarchical organization of the kinase domain that facilitates the orthogonal evolution of regulatory inputs and substrate outputs while maintaining catalytic function. We find that three quasi-independent "sectors"-groups of evolutionarily coupled residues-represent functional units in the kinase domain that encode for catalytic activity, substrate specificity, and regulation. Sector positions impact both disease and pharmacology: the catalytic sector is significantly enriched for somatic cancer mutations, and residues in the regulatory sector interact with allosteric kinase inhibitors. We propose that this functional architecture endows the kinase domain with inherent regulatory plasticity.
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Affiliation(s)
- Pau Creixell
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jai P Pandey
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Moitrayee Bhattacharyya
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Marc Creixell
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rama Ranganathan
- Center for Physics of Evolving Systems, Department of Biochemistry and Molecular Biology, Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - David Pincus
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
| | - Michael B Yaffe
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Surgery, Beth Israel Deaconess Medical Center, Divisions of Acute Care Surgery, Trauma, and Critical Care and Surgical Oncology, Harvard Medical School, Boston 02215, USA.
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38
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Wang P, Liang J, Shi LZ, Wang Y, Zhang P, Ouyang M, Preece D, Peng Q, Shao L, Fan J, Sun J, Li SS, Berns MW, Zhao H, Wang Y. Visualizing Spatiotemporal Dynamics of Intercellular Mechanotransmission upon Wounding. ACS PHOTONICS 2018; 5:3565-3574. [PMID: 31069245 PMCID: PMC6502247 DOI: 10.1021/acsphotonics.8b00383] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
During cell-to-cell communications, the interplay between physical and biochemical cues is essential for informational exchange and functional coordination, especially in multicellular organisms. However, it remains a challenge to visualize intercellular signaling dynamics in single live cells. Here, we report a photonic approach, based on laser microscissors and Förster resonance energy transfer (FRET) microscopy, to study intercellular signaling transmission. First, using our high-throughput screening platform, we developed a highly sensitive FRET-based biosensor (SCAGE) for Src kinase, a key regulator of intercellular interactions and signaling cascades. Notably, SCAGE showed a more than 40-fold sensitivity enhancement than the original biosensor in live mammalian cells. Next, upon local severance of physical intercellular connections by femtosecond laser pulses, SCAGE enabled the visualization of a transient Src activation across neighboring cells. Lastly, we found that this observed transient Src activation following the loss of cell-cell contacts depends on the passive structural support of cytoskeleton but not on the active actomyosin contractility. Hence, by precisely introducing local physical perturbations and directly visualizing spatiotemporal transmission of ensuing signaling events, our integrated approach could be broadly applied to mimic and investigate the wounding process at single-cell resolutions. This integrated approach with highly sensitive FRET-based biosensors provides a unique system to advance our in-depth understanding of molecular mechanisms underlying the physical-biochemical basis of intercellular coupling and wounding processes.
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Affiliation(s)
- Pengzhi Wang
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Jing Liang
- Department of Chemical and Biomolecular Engineering and Carl R. Woese Institute for Genomic Biology
| | - Linda Z. Shi
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Yi Wang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ping Zhang
- Institute of Mechanobiology and Biomedical Engineering, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingxing Ouyang
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Daryl Preece
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Qin Peng
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Lunan Shao
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Jason Fan
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Jie Sun
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shawn S. Li
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario Canada N6A 5C1
- Children’s Health Research Institute, 800 Commissioners Road East, London, Ontario Canada N6C 2 V5
| | - Michael W. Berns
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
- Beckman Laser Institute and Medical Clinic, University of California, Irvine, California 92612, United States
- Department of Developmental and Cell Biology, School of Biological Sciences, and Department of Biomedical Engineering, University of California, Irvine, Irvine, California 92617, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering and Carl R. Woese Institute for Genomic Biology
| | - Yingxiao Wang
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
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Wang R, Leung PYM, Huang F, Tang Q, Kaneko T, Huang M, Li Z, Li SSC, Wang Y, Xia J. Reverse Binding Mode of Phosphotyrosine Peptides with SH2 Protein. Biochemistry 2018; 57:5257-5269. [PMID: 30091902 DOI: 10.1021/acs.biochem.8b00677] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Discerning the different interaction states during dynamic protein-ligand binding is difficult. Here we apply site-specific cysteine-α-chloroacetyl cross-linking to scrutinize the binding between the Src homology 2 (SH2) domain and phosphotyrosine (pY) peptides, a highly dynamic interaction that is a key to cellular signal transduction. From a model SH2 protein to a set of representative SH2 domains, we showed here that a proximity-induced cysteine-α-chloroacetyl reaction cross-linked two spatially adjacent chemical groups as a result of the binding interaction, and reciprocally, the information about the interaction states can be deduced from the cross-linked products. To our surprise, we found SH2 domains can adopt a reverse binding mode with "single-pronged", "two-pronged", and "half" pY peptides. This finding was further supported by a set of 500 ns molecular dynamics simulations. This serendipitous finding defies the canonical theory of SH2 binding, suggests a possible answer about the source of the versatility of SH2 signaling, and sets a model for other protein binding interactions.
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Affiliation(s)
- Rui Wang
- Department of Biochemistry and Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry , Western University , London , Ontario N6A 5C1 , Canada
| | | | | | | | - Tomonori Kaneko
- Department of Biochemistry and Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry , Western University , London , Ontario N6A 5C1 , Canada
| | - Mei Huang
- Department of Biochemistry and Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry , Western University , London , Ontario N6A 5C1 , Canada
| | - Zigang Li
- School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen 518055 , China
| | - Shawn S C Li
- Department of Biochemistry and Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry , Western University , London , Ontario N6A 5C1 , Canada
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40
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Deep mutational analysis reveals functional trade-offs in the sequences of EGFR autophosphorylation sites. Proc Natl Acad Sci U S A 2018; 115:E7303-E7312. [PMID: 30012625 PMCID: PMC6077704 DOI: 10.1073/pnas.1803598115] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Upon activation, the epidermal growth factor receptor (EGFR) phosphorylates tyrosine residues in its cytoplasmic tail, which triggers the binding of Src homology 2 (SH2) and phosphotyrosine-binding (PTB) domains and initiates downstream signaling. The sequences flanking the tyrosine residues (referred to as "phosphosites") must be compatible with phosphorylation by the EGFR kinase domain and the recruitment of adapter proteins, while minimizing phosphorylation that would reduce the fidelity of signal transmission. To understand how phosphosite sequences encode these functions within a small set of residues, we carried out high-throughput mutational analysis of three phosphosite sequences in the EGFR tail. We used bacterial surface display of peptides coupled with deep sequencing to monitor phosphorylation efficiency and the binding of the SH2 and PTB domains of the adapter proteins Grb2 and Shc1, respectively. We found that the sequences of phosphosites in the EGFR tail are restricted to a subset of the range of sequences that can be phosphorylated efficiently by EGFR. Although efficient phosphorylation by EGFR can occur with either acidic or large hydrophobic residues at the -1 position with respect to the tyrosine, hydrophobic residues are generally excluded from this position in tail sequences. The mutational data suggest that this restriction results in weaker binding to adapter proteins but also disfavors phosphorylation by the cytoplasmic tyrosine kinases c-Src and c-Abl. Our results show how EGFR-family phosphosites achieve a trade-off between minimizing off-pathway phosphorylation and maintaining the ability to recruit the diverse complement of effectors required for downstream pathway activation.
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41
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Abstract
Creolimax fragrantissima is a member of the ichthyosporean clade, the earliest branching holozoan lineage. The kinome of Creolimax is markedly reduced as compared to those of metazoans. In particular, Creolimax possesses a single non-receptor tyrosine kinase: CfrSrc, the homolog of c-Src kinase. CfrSrc is an active tyrosine kinase, and it is expressed throughout the lifecycle of Creolimax. In animal cells, the regulatory mechanism for Src involves tyrosine phosphorylation at a C-terminal site by Csk kinase. The lack of Csk in Creolimax suggests that a different mode of negative regulation must exist for CfrSrc. We demonstrate that CfrPTP-3, one of the 7 tyrosine-specific phosphatases (PTPs) in Creolimax, suppresses CfrSrc activity in vitro and in vivo. Transcript levels of CfrPTP-3 and two other PTPs are significantly higher than that of CfrSrc in the motile amoeboid and sessile multinucleate stages of the Creolimax life cycle. Thus, in the context of a highly reduced kinome, a pre-existing PTP may have been co-opted for the role of Src regulation. Creolimax represents a unique model system to study the adaptation of tyrosine kinase signaling and regulatory mechanisms.
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42
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Shah NH, Löbel M, Weiss A, Kuriyan J. Fine-tuning of substrate preferences of the Src-family kinase Lck revealed through a high-throughput specificity screen. eLife 2018; 7:35190. [PMID: 29547119 PMCID: PMC5889215 DOI: 10.7554/elife.35190] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 03/15/2018] [Indexed: 01/04/2023] Open
Abstract
The specificity of tyrosine kinases is attributed predominantly to localization effects dictated by non-catalytic domains. We developed a method to profile the specificities of tyrosine kinases by combining bacterial surface-display of peptide libraries with next-generation sequencing. Using this, we showed that the tyrosine kinase ZAP-70, which is critical for T cell signaling, discriminates substrates through an electrostatic selection mechanism encoded within its catalytic domain (Shah et al., 2016). Here, we expand this high-throughput platform to analyze the intrinsic specificity of any tyrosine kinase domain against thousands of peptides derived from human tyrosine phosphorylation sites. Using this approach, we find a difference in the electrostatic recognition of substrates between the closely related Src-family kinases Lck and c-Src. This divergence likely reflects the specialization of Lck to act in concert with ZAP-70 in T cell signaling. These results point to the importance of direct recognition at the kinase active site in fine-tuning specificity.
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Affiliation(s)
- Neel H Shah
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Mark Löbel
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Arthur Weiss
- Department of Medicine, Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
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43
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Xu M, Zheng M, Liu G, Zhang M, Kang J. Screening of break point cluster region Abelson tyrosine kinase inhibitors by capillary electrophoresis. J Chromatogr A 2018; 1537:128-134. [DOI: 10.1016/j.chroma.2018.01.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/05/2018] [Accepted: 01/08/2018] [Indexed: 12/31/2022]
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Abstract
Medullary thyroid cancer (MTC) is a relatively uncommon yet prognostically significant thyroid cancer. Several recent advances in the biology and current or potential treatment of MTC are notable. These include a new understanding of the developmental biology of the thyroid C cell, which heretofore was thought to develop from the neural crest. RET, encoded by the most common driver gene in MTC, has been shown to be a dual function kinase, thus expanding its potential substrate repertoire. Promising new therapeutic developments are occurring; many have recently progressed to clinical development. There are new insights into RET inhibitor therapy for MTC. New strategies are being developed to inhibit the RAS proteins, which are potential therapeutic targets in MTC. Potential emerging immunotherapies for MTC are discussed. However, gaps in our knowledge of the basic biology of the C cell, its transformation to MTC, and the mechanisms of resistance to therapy impede progress; further research in these areas would have a substantial impact on the field.
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Affiliation(s)
- Barry Nelkin
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, 1650 Orleans Street, Baltimore, MD, 21287, USA
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45
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Fayer EL, Gilliland WM, Ramsey JM, Allbritton NL, Waters ML. N-Gemini peptides: cytosolic protease resistance via N-terminal dimerization of unstructured peptides. Chem Commun (Camb) 2017; 54:204-207. [PMID: 29230440 DOI: 10.1039/c7cc06819k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein we describe a synthetically simple strategy for increasing the lifetime of unstructured peptides in cytosolic environment via dimerization at the N-terminus to block threading into the catalytic cleft of cytosolic proteases. We establish this approach with kinase substrates, allowing for phosphorylation in cells as a demonstration of protease resistance.
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Affiliation(s)
- Effrat L Fayer
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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46
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Abstract
Innate immune cells sense danger through a plethora of germline-encoded receptors that recognize pathogen-associated molecular patterns (PAMPs) or cellular molecules that are exposed only by stressed, infected, malignant, or dead cells. Many of these danger-sensing receptors belong to the C-type lectin-like superfamily (CLSF) and therefore are called C-type lectin-like receptors (CTLRs). Certain activating CTLRs, namely, CLEC-2, Dectin-1, DNGR-1, NKp80, and NKp65, which are encoded by genes that are clustered together in a subregion of the mammalian natural killer gene complex (NKC), use a single copy tyrosine signaling module termed the hemi-immunoreceptor tyrosine-based activation motif (hemITAM). These hemITAM-bearing CTLRs are present on myeloid cells and innate lymphocytes and stimulate various functions, such as phagocytosis, cytokine production, and cytotoxicity. Proximal signaling mechanisms involve the tyrosine phosphorylation of the hemITAM and the subsequent activation of the kinase Syk. Signaling and Syk recruitment by the hemITAM appear to be tuned by variable amino acids within or near the hemITAM, which give rise to differences in downstream signaling events and diverging functional outcomes among hemITAM-bearing receptors.
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Affiliation(s)
- Björn Bauer
- Institute for Molecular Medicine, Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Alexander Steinle
- Institute for Molecular Medicine, Goethe-University Frankfurt am Main, Frankfurt am Main, Germany.
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47
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Delle Bovi RJ, Miller WT. Expression and purification of functional insulin and insulin-like growth factor 1 holoreceptors from mammalian cells. Anal Biochem 2017; 536:69-77. [PMID: 28830678 PMCID: PMC5701837 DOI: 10.1016/j.ab.2017.08.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/16/2017] [Accepted: 08/17/2017] [Indexed: 12/25/2022]
Abstract
The insulin receptor (IR) and insulin-like growth factor 1 receptor (IGF1R) are receptor tyrosine kinases (RTKs) involved in the regulation of many important cellular processes. The current proposed models of activation are derived from structural studies using soluble extracellular domains and cytoplasmic tyrosine kinase domains. Preparations of full length IR and IGF1R have been hampered by the need for unconventional affinity chromatography resins and/or harsh eluting conditions. Here, we present a purification protocol to obtain full-length, detergent solubilized IR and IGF1R at quantities suitable for biochemical and structural characterization. We screened a panel of 24 structurally diverse detergents for optimal ligand activation. The receptors purified in n-dodecyl-β-D-maltoside showed ligand-stimulated autophosphorylation and kinase activity, suggesting an intact transmembrane signaling mechanism. This convenient purification protocol can be used to produce high quantities of IR, IGF1R, or other RTKs, and can be adapted for other challenging membrane proteins.
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MESH Headings
- Antigens, CD/genetics
- Antigens, CD/isolation & purification
- Antigens, CD/metabolism
- Chromatography, Affinity
- HEK293 Cells
- Humans
- Receptor, IGF Type 1
- Receptor, Insulin/genetics
- Receptor, Insulin/isolation & purification
- Receptor, Insulin/metabolism
- Receptors, Somatomedin/genetics
- Receptors, Somatomedin/isolation & purification
- Receptors, Somatomedin/metabolism
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Affiliation(s)
- Richard J Delle Bovi
- Department of Physiology and Biophysics, Stony Brook University, NY, United States.
| | - W Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, NY, United States; Department of Veterans Affairs Medical Center, Northport, NY, United States.
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48
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Yuan H, Xi R, Chen C, Deng M. Differential network analysis via lasso penalized D-trace loss. Biometrika 2017. [DOI: 10.1093/biomet/asx049] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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49
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Wu C, Zheng Z, Guo Y, Tian C, Xue Q, Liang G. Fluorine substitution enhances the self-assembling ability of hydrogelators. NANOSCALE 2017; 9:11429-11433. [PMID: 28770916 DOI: 10.1039/c7nr02499a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
When supramolecular hydrogels are applied as tissue culture scaffolds, their mechanical strength and biocompatibility are the two most important factors that must be considered. However, systematic studies on the structure-mechanical property (or structure-cytotoxicity) relationship of hydrogels are rare. Herein, we rationally designed three hydrogelators and their corresponding phosphate precursors, and systematically studied their self-assembling ability and cytotoxicity. The results indicated that fluorine substitution, but not trifluoromethyl substitution with more fluorine atoms, to the phenylalanine motif enhanced the self-assembling ability and cytotoxicity of the hydrogelators (or precursors). We envision that our preliminary study of hydrogelator fluorination would provide a strategy for the development of supramolecular hydrogels for wider biomedical applications.
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Affiliation(s)
- Chengfan Wu
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China.
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50
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Saarbach J, Lindberg E, Folliet S, Georgeon S, Hantschel O, Winssinger N. Kinase-templated abiotic reaction. Chem Sci 2017; 8:5119-5125. [PMID: 28970898 PMCID: PMC5615226 DOI: 10.1039/c7sc01416c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/20/2017] [Indexed: 12/16/2022] Open
Abstract
Protein kinases are quintessential regulators of cellular function. Numerous pathologies are intimately linked to the dysregulated activity of a particular protein kinase. Herein we report a technology based on a proximity-induced chemical transformation that enables the detection and imaging of specific kinases. Using two probes that target the nucleotide-binding site and substrate binding site of a target kinase respectively, the reagents appended on the probes are brought within reactive distance thereby enabling the chemical transformation. The reaction used for sensing is a ruthenium-photocatalyzed reduction of a pyridinium immolative linker, which uncages a fluorophore (rhodamine). We demonstrate that this technology can be used to discriminate between closely related kinases with a high signal to noise ratio. We further demonstrate that the technology operates within the complexity of a cellular context with a good correlation between the level of kinase activity and fluorescence output.
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Affiliation(s)
- J Saarbach
- Faculty of Science , Department of Organic Chemistry , NCCR Chemical Biology , University of Geneva , 30 quai Ernest Ansermet , Geneva , Switzerland .
| | - E Lindberg
- Faculty of Science , Department of Organic Chemistry , NCCR Chemical Biology , University of Geneva , 30 quai Ernest Ansermet , Geneva , Switzerland .
| | - S Folliet
- Faculty of Science , Department of Organic Chemistry , NCCR Chemical Biology , University of Geneva , 30 quai Ernest Ansermet , Geneva , Switzerland .
| | - S Georgeon
- Swiss Institute for Experimental Cancer Research (ISREC) , NCCR Chemical Biology , School of Life Sciences , École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - O Hantschel
- Swiss Institute for Experimental Cancer Research (ISREC) , NCCR Chemical Biology , School of Life Sciences , École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - N Winssinger
- Faculty of Science , Department of Organic Chemistry , NCCR Chemical Biology , University of Geneva , 30 quai Ernest Ansermet , Geneva , Switzerland .
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