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Bradley D, Garand C, Belda H, Gagnon-Arsenault I, Treeck M, Elowe S, Landry CR. The substrate quality of CK2 target sites has a determinant role on their function and evolution. Cell Syst 2024; 15:544-562.e8. [PMID: 38861992 DOI: 10.1016/j.cels.2024.05.005] [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: 07/03/2023] [Revised: 02/29/2024] [Accepted: 05/20/2024] [Indexed: 06/13/2024]
Abstract
Most biological processes are regulated by signaling modules that bind to short linear motifs. For protein kinases, substrates may have full or only partial matches to the kinase recognition motif, a property known as "substrate quality." However, it is not clear whether differences in substrate quality represent neutral variation or if they have functional consequences. We examine this question for the kinase CK2, which has many fundamental functions. We show that optimal CK2 sites are phosphorylated at maximal stoichiometries and found in many conditions, whereas minimal substrates are more weakly phosphorylated and have regulatory functions. Optimal CK2 sites tend to be more conserved, and substrate quality is often tuned by selection. For intermediate sites, increases or decreases in substrate quality may be deleterious, as we demonstrate for a CK2 substrate at the kinetochore. The results together suggest a strong role for substrate quality in phosphosite function and evolution. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- David Bradley
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec City, QC G1V 0A6, Canada; Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec City, QC G1V 0A6, Canada; Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada.
| | - Chantal Garand
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec City, QC G1V 0A6, Canada; Axe de Reproduction, Santé de la mère et de l'enfant, CHU de Québec, Université Laval, Québec City, QC, Canada
| | - Hugo Belda
- Signalling in Host-Pathogen Interaction Laboratory, The Francis Crick Institute, London NW11AT, UK
| | - Isabelle Gagnon-Arsenault
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec City, QC G1V 0A6, Canada; Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec City, QC G1V 0A6, Canada; Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Moritz Treeck
- Signalling in Host-Pathogen Interaction Laboratory, The Francis Crick Institute, London NW11AT, UK; Cell Biology of Host-Pathogen Interaction Laboratory, The Gulbenkian Institute of Science, Oeiras 2780-156, Portugal
| | - Sabine Elowe
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec City, QC G1V 0A6, Canada; Axe de Reproduction, Santé de la mère et de l'enfant, CHU de Québec, Université Laval, Québec City, QC, Canada; Department of Pediatrics, Faculty of Medicine, Université Laval, Québec City, QC, Canada; Centre de Recherche sur le Cancer, CHU de Québec, Université Laval, Québec City, QC, Canada
| | - Christian R Landry
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec City, QC G1V 0A6, Canada; Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec City, QC G1V 0A6, Canada; Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada.
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2
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Zhang J, Yin G, Ye C, Feng M, Ji C, Zhou W, Wang F, Yu L, Huang S, Yu Z. Pyrotinib is effective in both trastuzumab-sensitive and primary resistant HER2-positive breast tumors. Chin J Cancer Res 2024; 36:124-137. [PMID: 38751436 PMCID: PMC11090794 DOI: 10.21147/j.issn.1000-9604.2024.02.03] [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: 12/14/2023] [Accepted: 02/29/2024] [Indexed: 05/18/2024] Open
Abstract
Objective Primary resistance to trastuzumab frequently occurs in human epidermal growth factor receptor 2 (HER2)-positive (+) breast cancer patients and remains a clinical challenge. Pyrotinib is a novel tyrosine kinase inhibitor that has shown efficacy in the treatment of HER2+ breast cancer. However, the efficacy of pyrotinib in HER2+ breast cancer with primary trastuzumab resistance is unknown. Methods HER2+ breast cancer cells sensitive or primarily resistant to trastuzumab were treated with trastuzumab, pyrotinib, or the combination. Cell proliferation, migration, invasion, and HER2 downstream signal pathways were analyzed. The effects of pyrotinib plus trastuzumab and pertuzumab plus trastuzumab were compared in breast cancer cells in vitro and a xenograft mouse model with primary resistance to trastuzumab. Results Pyrotinib had a therapeutic effect on trastuzumab-sensitive HER2+ breast cancer cells by inhibiting phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT) and rat sarcoma virus (RAS)/rapidly accelerated fibrosarcoma (RAF)/mitogen-activated protein kinase (MAPK)/extracellular-signal regulated kinase (ERK) pathways. In primary trastuzumab-resistant cells, pyrotinib inhibited cell growth, migration, invasion, and HER2 downstream pathways, whereas trastuzumab had no effects. The combination with trastuzumab did not show increased effects compared with pyrotinib alone. Compared with pertuzumab plus trastuzumab, pyrotinib plus trastuzumab was more effective in inhibiting cell proliferation and HER2 downstream pathways in breast cancer cells and tumor growth in a trastuzumab-resistant HER2+ breast cancer xenograft model. Conclusions Pyrotinib-containing treatments exhibited anti-cancer effects in HER2+ breast cancer cells sensitive and with primary resistance to trastuzumab. Notably, pyrotinib plus trastuzumab was more effective than trastuzumab plus pertuzumab in inhibiting tumor growth and HER2 downstream pathways in HER2+ breast cancer with primary resistance to trastuzumab. These findings support clinical testing of the therapeutic efficacy of dual anti-HER2 treatment combining an intracellular small molecule with an extracellular antibody.
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Affiliation(s)
- Jialin Zhang
- Department of Breast Surgery, the Second Hospital of Shandong University, Jinan 250033, China
| | - Gengshen Yin
- Department of Breast Surgery, the Second Hospital of Shandong University, Jinan 250033, China
| | - Chunmiao Ye
- Department of Breast Surgery, the Second Hospital of Shandong University, Jinan 250033, China
- Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan 250033, China
- Shandong Provincial Engineering Laboratory of Translational Research on Prevention and Treatment of Breast Disease, Jinan 250033, China
| | - Man Feng
- Department of Pathology, the Third Affiliated Hospital of Shandong First Medical University (Affiliated Hospital of Shandong Academy of Medical Sciences), Jinan 250031, China
| | - Changhua Ji
- Department of Pathology, the Second Hospital of Shandong University, Jinan 250033, China
| | - Wenzhong Zhou
- Department of Breast Surgery, the Second Hospital of Shandong University, Jinan 250033, China
- Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan 250033, China
- Shandong Provincial Engineering Laboratory of Translational Research on Prevention and Treatment of Breast Disease, Jinan 250033, China
| | - Fei Wang
- Department of Breast Surgery, the Second Hospital of Shandong University, Jinan 250033, China
- Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan 250033, China
- Shandong Provincial Engineering Laboratory of Translational Research on Prevention and Treatment of Breast Disease, Jinan 250033, China
| | - Lixiang Yu
- Department of Breast Surgery, the Second Hospital of Shandong University, Jinan 250033, China
- Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan 250033, China
- Shandong Provincial Engineering Laboratory of Translational Research on Prevention and Treatment of Breast Disease, Jinan 250033, China
| | - Shuya Huang
- Department of Breast Surgery, the Second Hospital of Shandong University, Jinan 250033, China
- Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan 250033, China
- Shandong Provincial Engineering Laboratory of Translational Research on Prevention and Treatment of Breast Disease, Jinan 250033, China
| | - Zhigang Yu
- Department of Breast Surgery, the Second Hospital of Shandong University, Jinan 250033, China
- Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan 250033, China
- Shandong Provincial Engineering Laboratory of Translational Research on Prevention and Treatment of Breast Disease, Jinan 250033, China
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3
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Szukiewicz D. CX3CL1 (Fractalkine)-CX3CR1 Axis in Inflammation-Induced Angiogenesis and Tumorigenesis. Int J Mol Sci 2024; 25:4679. [PMID: 38731899 PMCID: PMC11083509 DOI: 10.3390/ijms25094679] [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: 03/28/2024] [Revised: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
The chemotactic cytokine fractalkine (FKN, chemokine CX3CL1) has unique properties resulting from the combination of chemoattractants and adhesion molecules. The soluble form (sFKN) has chemotactic properties and strongly attracts T cells and monocytes. The membrane-bound form (mFKN) facilitates diapedesis and is responsible for cell-to-cell adhesion, especially by promoting the strong adhesion of leukocytes (monocytes) to activated endothelial cells with the subsequent formation of an extracellular matrix and angiogenesis. FKN signaling occurs via CX3CR1, which is the only known member of the CX3C chemokine receptor subfamily. Signaling within the FKN-CX3CR1 axis plays an important role in many processes related to inflammation and the immune response, which often occur simultaneously and overlap. FKN is strongly upregulated by hypoxia and/or inflammation-induced inflammatory cytokine release, and it may act locally as a key angiogenic factor in the highly hypoxic tumor microenvironment. The importance of the FKN/CX3CR1 signaling pathway in tumorigenesis and cancer metastasis results from its influence on cell adhesion, apoptosis, and cell migration. This review presents the role of the FKN signaling pathway in the context of angiogenesis in inflammation and cancer. The mechanisms determining the pro- or anti-tumor effects are presented, which are the cause of the seemingly contradictory results that create confusion regarding the therapeutic goals.
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Affiliation(s)
- Dariusz Szukiewicz
- Department of Biophysics, Physiology & Pathophysiology, Faculty of Health Sciences, Medical University of Warsaw, 02-004 Warsaw, Poland
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4
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Sexton JA, Potchernikov T, Bibeau JP, Casanova-Sepúlveda G, Cao W, Lou HJ, Boggon TJ, De La Cruz EM, Turk BE. Distinct functional constraints driving conservation of the cofilin N-terminal regulatory tail. Nat Commun 2024; 15:1426. [PMID: 38365893 PMCID: PMC10873347 DOI: 10.1038/s41467-024-45878-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Abstract
Cofilin family proteins have essential roles in remodeling the cytoskeleton through filamentous actin depolymerization and severing. The short, unstructured N-terminal region of cofilin is critical for actin binding and harbors the major site of inhibitory phosphorylation. Atypically for a disordered sequence, the N-terminal region is highly conserved, but specific aspects driving this conservation are unclear. Here, we screen a library of 16,000 human cofilin N-terminal sequence variants for their capacity to support growth in S. cerevisiae in the presence or absence of the upstream regulator LIM kinase. Results from the screen and biochemical analysis of individual variants reveal distinct sequence requirements for actin binding and regulation by LIM kinase. LIM kinase recognition only partly explains sequence constraints on phosphoregulation, which are instead driven to a large extent by the capacity for phosphorylation to inactivate cofilin. We find loose sequence requirements for actin binding and phosphoinhibition, but collectively they restrict the N-terminus to sequences found in natural cofilins. Our results illustrate how a phosphorylation site can balance potentially competing sequence requirements for function and regulation.
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Affiliation(s)
- Joel A Sexton
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Tony Potchernikov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Jeffrey P Bibeau
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | | | - Wenxiang Cao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Titus J Boggon
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Enrique M De La Cruz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, 06520, USA.
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5
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Nocka LM, Eisen TJ, Iavarone AT, Groves JT, Kuriyan J. Stimulation of the catalytic activity of the tyrosine kinase Btk by the adaptor protein Grb2. eLife 2023; 12:e82676. [PMID: 37159508 PMCID: PMC10132808 DOI: 10.7554/elife.82676] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 04/03/2023] [Indexed: 05/11/2023] Open
Abstract
The Tec-family kinase Btk contains a lipid-binding Pleckstrin homology and Tec homology (PH-TH) module connected by a proline-rich linker to a 'Src module', an SH3-SH2-kinase unit also found in Src-family kinases and Abl. We showed previously that Btk is activated by PH-TH dimerization, which is triggered on membranes by the phosphatidyl inositol phosphate PIP3, or in solution by inositol hexakisphosphate (IP6) (Wang et al., 2015, https://doi.org/10.7554/eLife.06074). We now report that the ubiquitous adaptor protein growth-factor-receptor-bound protein 2 (Grb2) binds to and substantially increases the activity of PIP3-bound Btk on membranes. Using reconstitution on supported-lipid bilayers, we find that Grb2 can be recruited to membrane-bound Btk through interaction with the proline-rich linker in Btk. This interaction requires intact Grb2, containing both SH3 domains and the SH2 domain, but does not require that the SH2 domain be able to bind phosphorylated tyrosine residues - thus Grb2 bound to Btk is free to interact with scaffold proteins via the SH2 domain. We show that the Grb2-Btk interaction recruits Btk to scaffold-mediated signaling clusters in reconstituted membranes. Our findings indicate that PIP3-mediated dimerization of Btk does not fully activate Btk, and that Btk adopts an autoinhibited state at the membrane that is released by Grb2.
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Affiliation(s)
- Laura M Nocka
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences, University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Timothy J Eisen
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Anthony T Iavarone
- California Institute for Quantitative Biosciences, University of California, BerkeleyBerkeleyUnited States
- College of Chemistry Mass Spectrometry Facility, University of California, BerkeleyBerkeleyUnited States
| | - Jay T Groves
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences, University of California, BerkeleyBerkeleyUnited States
- Institute for Digital Molecular Analytics and Science, Nanyang Technological UniversitySingaporeSingapore
| | - John Kuriyan
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences, University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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6
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Wei H, Li X. Deep mutational scanning: A versatile tool in systematically mapping genotypes to phenotypes. Front Genet 2023; 14:1087267. [PMID: 36713072 PMCID: PMC9878224 DOI: 10.3389/fgene.2023.1087267] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/02/2023] [Indexed: 01/13/2023] Open
Abstract
Unveiling how genetic variations lead to phenotypic variations is one of the key questions in evolutionary biology, genetics, and biomedical research. Deep mutational scanning (DMS) technology has allowed the mapping of tens of thousands of genetic variations to phenotypic variations efficiently and economically. Since its first systematic introduction about a decade ago, we have witnessed the use of deep mutational scanning in many research areas leading to scientific breakthroughs. Also, the methods in each step of deep mutational scanning have become much more versatile thanks to the oligo-synthesizing technology, high-throughput phenotyping methods and deep sequencing technology. However, each specific possible step of deep mutational scanning has its pros and cons, and some limitations still await further technological development. Here, we discuss recent scientific accomplishments achieved through the deep mutational scanning and describe widely used methods in each step of deep mutational scanning. We also compare these different methods and analyze their advantages and disadvantages, providing insight into how to design a deep mutational scanning study that best suits the aims of the readers' projects.
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Affiliation(s)
- Huijin Wei
- Zhejiang University—University of Edinburgh Institute, Zhejiang University, Haining, Zhejiang, China
| | - Xianghua Li
- Zhejiang University—University of Edinburgh Institute, Zhejiang University, Haining, Zhejiang, China,Deanery of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom,The Second Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang, China,Biomedical and Health Translational Centre of Zhejiang Province, Haining, Zhejiang, China,*Correspondence: Xianghua Li,
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7
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Renu K, Vinayagam S, Veeraraghavan VP, Mukherjee AG, Wanjari UR, Prabakaran DS, Ganesan R, Dey A, Vellingiri B, Kandasamy S, Ramanathan G, Doss C GP, George A, Gopalakrishnan AV. Molecular Crosstalk between the Immunological Mechanism of the Tumor Microenvironment and Epithelial–Mesenchymal Transition in Oral Cancer. Vaccines (Basel) 2022; 10:vaccines10091490. [PMID: 36146567 PMCID: PMC9504083 DOI: 10.3390/vaccines10091490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 11/30/2022] Open
Abstract
Oral cancer is a significant non-communicable disease affecting both emergent nations and developed countries. Squamous cell carcinoma of the head and neck represent the eight major familiar cancer types worldwide, accounting for more than 350,000 established cases every year. Oral cancer is one of the most exigent tumors to control and treat. The survival rate of oral cancer is poor due to local invasion along with recurrent lymph node metastasis. The tumor microenvironment contains a different population of cells, such as fibroblasts associated with cancer, immune-infiltrating cells, and other extracellular matrix non-components. Metastasis in a primary site is mainly due to multifaceted progression known as epithelial-to-mesenchymal transition (EMT). For the period of EMT, epithelial cells acquire mesenchymal cell functional and structural characteristics, which lead to cell migration enhancement and promotion of the dissemination of tumor cells. The present review links the tumor microenvironment and the role of EMT in inflammation, transcriptional factors, receptor involvement, microRNA, and other signaling events. It would, in turn, help to better understand the mechanism behind the tumor microenvironment and EMT during oral cancer.
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Affiliation(s)
- Kaviyarasi Renu
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, Tamil Nadu, India
- Correspondence: (K.R.); (A.V.G.)
| | - Sathishkumar Vinayagam
- Department of Biotechnology, Centre for Postgraduate and Research Studies, Periyar University, Dharmapuri 635205, Tamil Nadu, India
| | - Vishnu Priya Veeraraghavan
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, Tamil Nadu, India
| | - Anirban Goutam Mukherjee
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Uddesh Ramesh Wanjari
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - D. S. Prabakaran
- Department of Radiation Oncology, College of Medicine, Chungbuk National University, Chungdae-ro 1, Seowon-gu, Cheongju 28644, Korea
- Department of Biotechnology, Ayya Nadar Janaki Ammal College (Autonomous), Srivilliputhur Main Road, Sivakasi 626124, Tamil Nadu, India
| | - Raja Ganesan
- Institute for Liver and Digestive Diseases, Hallym University, Chuncheon 24252, Korea
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata 700073, West Bengal, India
| | - Balachandar Vellingiri
- Human Molecular Cytogenetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore 641046, Tamil Nadu, India
| | - Sabariswaran Kandasamy
- Institute of Energy Research, Jiangsu University, No 301, Xuefu Road, Zhenjiang 212013, China
| | - Gnanasambandan Ramanathan
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - George Priya Doss C
- Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Alex George
- Jubilee Centre for Medical Research, Jubilee Mission Medical College and Research Institute, Thrissur 680005, Kerala, India
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
- Correspondence: (K.R.); (A.V.G.)
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8
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The evolution of post-translational modifications. Curr Opin Genet Dev 2022; 76:101956. [PMID: 35843204 DOI: 10.1016/j.gde.2022.101956] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/14/2022] [Accepted: 06/20/2022] [Indexed: 11/20/2022]
Abstract
Post-translational modifications (PTMs) are chemical modifications that can regulate the activity and function of proteins. From an evolutionary perspective, they also represent a fast mechanism for the generation of phenotypic diversity and divergence. Advances in mass spectrometry have now enabled the identification of over 600 distinct PTM classes collectively spanning an order of 106 unique sites. However, the chemical detection of PTMs has lagged far behind their functional characterisation, and relatively little is still known about the selective constraints that govern PTM evolution. In particular, the true fraction of PTM sites that are functional - and thus subject to selection - remains an open question. Here, I review advances made in the past two years towards understanding the evolution of PTMs and their associated enzymes.
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9
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A two-component protein condensate of the EGFR cytoplasmic tail and Grb2 regulates Ras activation by SOS at the membrane. Proc Natl Acad Sci U S A 2022; 119:e2122531119. [PMID: 35507881 PMCID: PMC9181613 DOI: 10.1073/pnas.2122531119] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
SignificanceTwo-dimensional condensates of proteins on the membrane surface, driven by tyrosine phosphorylation, are beginning to emerge as important players in signal transduction. This work describes discovery of a protein condensation phase transition of EGFR and Grb2 on membrane surfaces, which is poised to have a significant impact on how we understand EGFR signaling and misregulation in disease. EGFR condensation is mediated through a Grb2-Grb2 crosslinking element, which itself is regulatable through a specific phosphotyrosine site on Grb2. Furthermore, the EGFR condensate exerts significant control over the ability of SOS to activate Ras, thus implicating the EGFR condensate as a regulator of signal propagation from EGFR to Ras and the MAPK pathway.
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10
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Scheele RA, Lindenburg LH, Petek M, Schober M, Dalby KN, Hollfelder F. Droplet-based screening of phosphate transfer catalysis reveals how epistasis shapes MAP kinase interactions with substrates. Nat Commun 2022; 13:844. [PMID: 35149678 PMCID: PMC8837617 DOI: 10.1038/s41467-022-28396-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 01/10/2022] [Indexed: 11/20/2022] Open
Abstract
The combination of ultrahigh-throughput screening and sequencing informs on function and intragenic epistasis within combinatorial protein mutant libraries. Establishing a droplet-based, in vitro compartmentalised approach for robust expression and screening of protein kinase cascades (>107 variants/day) allowed us to dissect the intrinsic molecular features of the MKK-ERK signalling pathway, without interference from endogenous cellular components. In a six-residue combinatorial library of the MKK1 docking domain, we identified 29,563 sequence permutations that allow MKK1 to efficiently phosphorylate and activate its downstream target kinase ERK2. A flexibly placed hydrophobic sequence motif emerges which is defined by higher order epistatic interactions between six residues, suggesting synergy that enables high connectivity in the sequence landscape. Through positive epistasis, MKK1 maintains function during mutagenesis, establishing the importance of co-dependent residues in mammalian protein kinase-substrate interactions, and creating a scenario for the evolution of diverse human signalling networks. Here, the authors use a droplet-based screen for phosphate transfer catalysis, testing variants of the human protein kinase MKK1 for its ability to activate its downstream target ERK2. Data reveal a flexible motif in the MKK1 docking domain that promotes efficient activation of ERK2, and suggest epistasis between the residues within that sequence.
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Affiliation(s)
- Remkes A Scheele
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | | | - Maya Petek
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.,Faculty of Medicine, University of Maribor, SI-2000, Maribor, Slovenia
| | - Markus Schober
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
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11
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Martin-Fernandez ML. Fluorescence Imaging of Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitor Resistance in Non-Small Cell Lung Cancer. Cancers (Basel) 2022; 14:cancers14030686. [PMID: 35158954 PMCID: PMC8833717 DOI: 10.3390/cancers14030686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/21/2022] [Accepted: 01/26/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Lung cancer is the leading cause of cancer-related deaths, with a low (<21%) 5-year survival rate. Lung cancer is often driven by the misfunction of molecules on the surface of cells of the epithelium, which orchestrate mechanisms by which these cells grow and proliferate. Beyond common non-specific treatments, such as chemotherapy or radiotherapy, among molecular-specific treatments, a number of small-molecule drugs that block cancer-driven molecular activity have been developed. These drugs initially have significant success in a subset of patients, but these patients systematically develop resistance within approximately one year of therapy. Substantial efforts towards understanding the mechanisms of resistance have focused on the genomics of cancer progression, the response of cells to the drugs, and the cellular changes that allow resistance to develop. Fluorescence microscopy of many flavours has significantly contributed to the last two areas, and is the subject of this review. Abstract Non-small cell lung cancer (NSCLC) is a complex disease often driven by activating mutations or amplification of the epidermal growth factor receptor (EGFR) gene, which expresses a transmembrane receptor tyrosine kinase. Targeted anti-EGFR treatments include small-molecule tyrosine kinase inhibitors (TKIs), among which gefitinib and erlotinib are the best studied, and their function more often imaged. TKIs block EGFR activation, inducing apoptosis in cancer cells addicted to EGFR signals. It is not understood why TKIs do not work in tumours driven by EGFR overexpression but do so in tumours bearing classical activating EGFR mutations, although the latter develop resistance in about one year. Fluorescence imaging played a crucial part in research efforts to understand pro-survival mechanisms, including the dysregulation of autophagy and endocytosis, by which cells overcome the intendedly lethal TKI-induced EGFR signalling block. At their core, pro-survival mechanisms are facilitated by TKI-induced changes in the function and conformation of EGFR and its interactors. This review brings together some of the main advances from fluorescence imaging in investigating TKI function and places them in the broader context of the TKI resistance field, highlighting some paradoxes and suggesting some areas where super-resolution and other emerging methods could make a further contribution.
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Affiliation(s)
- Marisa L Martin-Fernandez
- Central Laser Facility, Science & Technology Facilities Council, Rutherford Appleton Laboratory, Didcot OX11 0FA, UK
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12
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Phosphorylation of TRIP13 at Y56 induces radiation resistance but sensitizes head and neck cancer to cetuximab. Mol Ther 2022; 30:468-484. [PMID: 34111559 PMCID: PMC8753291 DOI: 10.1016/j.ymthe.2021.06.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 03/10/2021] [Accepted: 06/01/2021] [Indexed: 01/07/2023] Open
Abstract
Radiation therapy, a mainstay of treatment for head and neck cancer, is not always curative due to the development of treatment resistance; additionally, multi-institutional trials have questioned the efficacy of concurrent radiation with cetuximab, the epidermal growth factor receptor (EGFR) inhibitor. We unraveled a mechanism for radiation resistance; that is, radiation induces EGFR, which phosphorylates TRIP13 (thyroid hormone receptor interactor 13) on tyrosine 56. Phosphorylated (phospho-)TRIP13 promotes non-homologous end joining (NHEJ) repair to induce radiation resistance. NHEJ is the main repair pathway for radiation-induced DNA damage. Tumors expressing high TRIP13 do not respond to radiation but are sensitive to cetuximab or cetuximab combined with radiation. Suppression of phosphorylation of TRIP13 at Y56 abrogates these effects. These findings show that EGFR-mediated phosphorylation of TRIP13 at Y56 is a vital mechanism of radiation resistance. Notably, TRIP13-pY56 could be used to predict the response to radiation or cetuximab and could be explored as an actionable target.
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13
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Horikawa M, Kakiuchi Y, Kashima D, Ogawa K, Kawahara M. Thrombopoietin receptor-based protein-protein interaction screening (THROPPIS). Biotechnol Bioeng 2021; 119:287-298. [PMID: 34708875 DOI: 10.1002/bit.27975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/20/2021] [Accepted: 10/23/2021] [Indexed: 12/12/2022]
Abstract
As protein-protein interactions (PPIs) are involved in many cellular events, development of mammalian cytosolic PPI detection systems is important for drug discovery as well as understanding biological phenomena. We have previously reported a c-kit-based PPI screening (KIPPIS) system, in which proteins of interest were fused with a receptor tyrosine kinase c-kit, leading to intracellular PPI-dependent cell growth. However, it has not been investigated whether PPI can be detected using other receptors. In this study, we employed a thrombopoietin receptor, which belongs to the Type I cytokine receptor family, to develop a thrombopoietin receptor-based PPI screening (THROPPIS) system. To improve the sensitivity of THROPPIS, we examined two strategies of (i) localization of the chimeric receptors on the cell membrane, and (ii) addition of a helper module to the chimeric receptors. Intriguingly, the nonlocalized chimeric receptor showed the best performance of THROPPIS. Furthermore, the addition of the helper module dramatically improved the detection sensitivity. In total, 5 peptide-domain interactions were detected successfully, demonstrating the versatility of THROPPIS. In addition, a peptide-domain interaction was detected even when insulin receptor or epidermal growth factor receptor was used as a signaling domain, demonstrating that this PPI detection system can be extended to other receptors.
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Affiliation(s)
- Makiko Horikawa
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yosuke Kakiuchi
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Daiki Kashima
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Kenichiro Ogawa
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Masahiro Kawahara
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,Laboratory of Cell Vaccine, Center for Vaccine and Adjuvant Research (CVAR), National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki-shi, Osaka, Japan
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14
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Min W, He C, Zhang S, Zhao Y. c-Src Increases the Sensitivity to TKIs in the EGFR-Mutant Lung Adenocarcinoma. Front Oncol 2021; 11:602900. [PMID: 34367939 PMCID: PMC8339729 DOI: 10.3389/fonc.2021.602900] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 06/23/2021] [Indexed: 11/29/2022] Open
Abstract
c-Src and the epidermal growth factor receptor (EGFR) are key apical kinases that govern cell responses to microenvironmental cues. How c-Src affects EGFR-related signaling and targeted therapy remains elusive. Initially, caspase-8 phosphorylated at tyrosine 380 by c-Src predominantly enhancing c-Src activation to facilitate metastasis through attaining epithelial-mesenchymal transition (EMT) phenotype in lung adenocarcinoma. Mechanistically, the linkage of c-Src SH2 domain with phosphotyrosine 380 of caspase-8 and SH3 domain with “PDEP” motif of caspase-8 overactivates c-Src as compared with other c-Src-partner proteins. c-Src is incapable of triggering EGFR-related signaling. This is reflected by the levels of phosphotyrosine 1068, 1086, and 1145, which have no impact on c-Src activation. Tyrosine kinase inhibitors (TKIs) suppress EGFR-related signaling to yield cell deaths of lung adenocarcinoma by both necroptosis and intrinsic apoptosis. Given that c-Src activation is frequent in lung adenocarcinoma, blocking c-Src activation through dasatinib can seal the survival-signaling-related phosphotyrosines of EGFR by its SH2 domain, which in turn increases the antitumor activity of TKIs in EGFR-mutant lung adenocarcinoma. Collectively, c-Src inactivation by dasatinib administration sensitizes EGFR-mutant lung adenocarcinoma to TKIs.
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Affiliation(s)
- Weili Min
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Chenyang He
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Shuqun Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yang Zhao
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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15
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York HM, Patil A, Moorthi UK, Kaur A, Bhowmik A, Hyde GJ, Gandhi H, Fulcher A, Gaus K, Arumugam S. Rapid whole cell imaging reveals a calcium-APPL1-dynein nexus that regulates cohort trafficking of stimulated EGF receptors. Commun Biol 2021; 4:224. [PMID: 33597720 PMCID: PMC7889693 DOI: 10.1038/s42003-021-01740-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 01/22/2021] [Indexed: 01/31/2023] Open
Abstract
The endosomal system provides rich signal processing capabilities for responses elicited by growth factor receptors and their ligands. At the single cell level, endosomal trafficking becomes a critical component of signal processing, as exemplified by the epidermal growth factor (EGF) receptors. Activated EGFRs are trafficked to the phosphatase-enriched peri-nuclear region (PNR), where they are dephosphorylated and degraded. The details of the mechanisms that govern the movements of stimulated EGFRs towards the PNR, are not completely known. Here, exploiting the advantages of lattice light-sheet microscopy, we show that EGFR activation by EGF triggers a transient calcium increase causing a whole-cell level redistribution of Adaptor Protein, Phosphotyrosine Interacting with PH Domain And Leucine Zipper 1 (APPL1) from pre-existing endosomes within one minute, the rebinding of liberated APPL1 directly to EGFR, and the dynein-dependent translocation of APPL1-EGF-bearing endosomes to the PNR within ten minutes. The cell spanning, fast acting network that we reveal integrates a cascade of events dedicated to the cohort movement of activated EGF receptors. Our findings support the intriguing proposal that certain endosomal pathways have shed some of the stochastic strategies of traditional trafficking and have evolved processes that provide the temporal predictability that typify canonical signaling.
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Affiliation(s)
- H. M. York
- grid.1002.30000 0004 1936 7857Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton/Melbourne, VIC Australia ,grid.1002.30000 0004 1936 7857European Molecular Biological Laboratory Australia (EMBL Australia), Monash University, Clayton/Melbourne, VIC Australia
| | - A. Patil
- grid.1002.30000 0004 1936 7857Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton/Melbourne, VIC Australia ,grid.1002.30000 0004 1936 7857European Molecular Biological Laboratory Australia (EMBL Australia), Monash University, Clayton/Melbourne, VIC Australia
| | - U. K. Moorthi
- grid.1002.30000 0004 1936 7857Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton/Melbourne, VIC Australia ,grid.1002.30000 0004 1936 7857European Molecular Biological Laboratory Australia (EMBL Australia), Monash University, Clayton/Melbourne, VIC Australia
| | - A. Kaur
- grid.1005.40000 0004 4902 0432Single Molecule Science, University of New South Wales, Sydney, Australia
| | - A. Bhowmik
- grid.1005.40000 0004 4902 0432Single Molecule Science, University of New South Wales, Sydney, Australia
| | | | - H. Gandhi
- grid.1002.30000 0004 1936 7857Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton/Melbourne, VIC Australia ,grid.1002.30000 0004 1936 7857European Molecular Biological Laboratory Australia (EMBL Australia), Monash University, Clayton/Melbourne, VIC Australia
| | - A. Fulcher
- grid.1002.30000 0004 1936 7857Monash Micro Imaging, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton/Melbourne, VIC Australia
| | - K. Gaus
- grid.1005.40000 0004 4902 0432Single Molecule Science, University of New South Wales, Sydney, Australia ,grid.1005.40000 0004 4902 0432ARC Centre of Excellence in Advanced Molecular Imaging, UNSW, Sydney, Australia
| | - S. Arumugam
- grid.1002.30000 0004 1936 7857Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton/Melbourne, VIC Australia ,grid.1002.30000 0004 1936 7857European Molecular Biological Laboratory Australia (EMBL Australia), Monash University, Clayton/Melbourne, VIC Australia ,grid.1005.40000 0004 4902 0432Single Molecule Science, University of New South Wales, Sydney, Australia ,grid.1005.40000 0004 4902 0432ARC Centre of Excellence in Advanced Molecular Imaging, UNSW, Sydney, Australia
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16
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Ling Z, Cheng B, Tao X. Epithelial-to-mesenchymal transition in oral squamous cell carcinoma: Challenges and opportunities. Int J Cancer 2020; 148:1548-1561. [PMID: 33091960 DOI: 10.1002/ijc.33352] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/08/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023]
Abstract
Oral squamous cell carcinoma (OSCC) is the most common malignancy representing 90% of all forms of oral cancer worldwide. Although great efforts have been made in the past decades, the 5-year survival rate of OSCC patients is no more than 60% due to tumor metastasis and subsequent recurrence. The metastasis from the primary site is due to a complex process known as epithelial-to-mesenchymal transition (EMT). During the EMT, epithelial cells gradually acquire the structural and functional characteristics of mesenchymal cells, leading to the upregulation of cell migration and the promotion of tumor cell dissemination. Therefore, EMT attracted broad attention due to its close relationship with cancer invasion and metastasis. Therefore, in the present review, an extensive description of the current research on OSCC and the role of EMT in this cancer type is provided, including diverse EMT markers, regulatory networks and crucial EMT-inducing transcription factors in OSCC. Moreover, a brief summary was made regarding the current application of EMT-correlated indexes in the prognostic analysis of OSCC patients, and the potential therapeutic approaches against OSCC and difficulties in the development of an effective anti-EMT treatment are discussed. Our aim is to provide novel insights to develop new strategies to combat OSCC by targeting EMT.
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Affiliation(s)
- Zihang Ling
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Bin Cheng
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Xiaoan Tao
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
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17
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You M, Xia X, Li H, Wu J, Rong R, Zeng Z, Xiong K, Huang J, Tang L, Lei H, Wu W, Ji D. Normal vitreous promotes angiogenesi via the epidermal growth factor receptor. FASEB J 2020; 34:14799-14809. [PMID: 32910506 DOI: 10.1096/fj.201902862rrr] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 08/16/2020] [Accepted: 08/23/2020] [Indexed: 11/11/2022]
Abstract
Vitreous, a transparent tissue in our body, contains anti-angiogenesis factors. Our previous work reported that vitreous activates the signaling pathway of epidermal growth factor receptor (EGFR), which plays a critical role in angiogenesis. The aim of this study was to determine the role of EGFR in vitreous-induced angiogenesis-related cellular responses in vitro. Using a pharmacologic and molecular approach, we found that vitreous increased proliferation and migration via EGFR in human umbilical vein endothelial cells (HUVECs). Furthermore, we demonstrated that vitreous promoted tube formation via EGFR in HUVECs. Subsequently, depletion of EGFR using CRISPR/Cas9 and blockage with EGFR inhibitor AG1478 suppressed vitreous-induced Akt activation and cell proliferation, migration, and tube formation in HUVECs. The significance of the angiogenic effect derived from vitreous demonstrates the importance of vitreous in the ocular physiology and the pathobiology of angiogenesis-related ophthalmic diseases, such as proliferative diabetic retinopathy.
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Affiliation(s)
- Mengling You
- Departments of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, P.R. China
| | - Xiaobo Xia
- Departments of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, P.R. China
| | - Haibo Li
- Departments of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, P.R. China
| | - Jiayu Wu
- School of Life Sciences, Central South University, Changsha, P.R. China
| | - Rong Rong
- Departments of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, P.R. China
| | - Zhou Zeng
- Departments of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, P.R. China
| | - Kun Xiong
- Department of Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha, P.R. China
| | - Jufang Huang
- Department of Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha, P.R. China
| | - Luosheng Tang
- Departments of Ophthalmology, the Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Hetian Lei
- Shenzhen Eye Hospital, Shenzhen Eye Institute, Shenzhen, P.R. China
| | - Wenyi Wu
- Departments of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, P.R. China
| | - Dan Ji
- Departments of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, P.R. China
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18
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Amacher JF, Brooks L, Hampton TH, Madden DR. Specificity in PDZ-peptide interaction networks: Computational analysis and review. JOURNAL OF STRUCTURAL BIOLOGY-X 2020; 4:100022. [PMID: 32289118 PMCID: PMC7138185 DOI: 10.1016/j.yjsbx.2020.100022] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/26/2020] [Accepted: 02/29/2020] [Indexed: 01/03/2023]
Abstract
Globular PDZ domains typically serve as protein-protein interaction modules that regulate a wide variety of cellular functions via recognition of short linear motifs (SLiMs). Often, PDZ mediated-interactions are essential components of macromolecular complexes, and disruption affects the entire scaffold. Due to their roles as linchpins in trafficking and signaling pathways, PDZ domains are attractive targets: both for controlling viral pathogens, which bind PDZ domains and hijack cellular machinery, as well as for developing therapies to combat human disease. However, successful therapeutic interventions that avoid off-target effects are a challenge, because each PDZ domain interacts with a number of cellular targets, and specific binding preferences can be difficult to decipher. Over twenty-five years of research has produced a wealth of data on the stereochemical preferences of individual PDZ proteins and their binding partners. Currently the field lacks a central repository for this information. Here, we provide this important resource and provide a manually curated, comprehensive list of the 271 human PDZ domains. We use individual domain, as well as recent genomic and proteomic, data in order to gain a holistic view of PDZ domains and interaction networks, arguing this knowledge is critical to optimize targeting selectivity and to benefit human health.
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Affiliation(s)
- Jeanine F Amacher
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.,Department of Chemistry, Western Washington University, Bellingham, WA 98225, USA
| | - Lionel Brooks
- Department of Biology, Western Washington University, Bellingham, WA 98225, USA
| | - Thomas H Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Dean R Madden
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
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19
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Esposito D, Weile J, Shendure J, Starita LM, Papenfuss AT, Roth FP, Fowler DM, Rubin AF. MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect. Genome Biol 2019; 20:223. [PMID: 31679514 PMCID: PMC6827219 DOI: 10.1186/s13059-019-1845-6] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 10/01/2019] [Indexed: 11/10/2022] Open
Abstract
Multiplex assays of variant effect (MAVEs), such as deep mutational scans and massively parallel reporter assays, test thousands of sequence variants in a single experiment. Despite the importance of MAVE data for basic and clinical research, there is no standard resource for their discovery and distribution. Here, we present MaveDB ( https://www.mavedb.org ), a public repository for large-scale measurements of sequence variant impact, designed for interoperability with applications to interpret these datasets. We also describe the first such application, MaveVis, which retrieves, visualizes, and contextualizes variant effect maps. Together, the database and applications will empower the community to mine these powerful datasets.
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Affiliation(s)
- Daniel Esposito
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Jochen Weile
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Anthony T Papenfuss
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
- Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
- Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, Australia
| | - Frederick P Roth
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada.
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Department of Computer Science, University of Toronto, Toronto, ON, Canada.
- Canadian Institute for Advanced Research, Toronto, ON, Canada.
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Canadian Institute for Advanced Research, Toronto, ON, Canada.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
| | - Alan F Rubin
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.
- Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
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20
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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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21
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Tiruthani K, Mischler A, Ahmed S, Mahinthakumar J, Haugh JM, Rao BM. Design and evaluation of engineered protein biosensors for live-cell imaging of EGFR phosphorylation. Sci Signal 2019; 12:eaap7584. [PMID: 31164479 PMCID: PMC8757379 DOI: 10.1126/scisignal.aap7584] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Live-cell fluorescence microscopy is broadly applied to study the dynamics of receptor-mediated cell signaling, but the availability of intracellular biosensors is limited. A biosensor based on the tandem SH2 domains from phospholipase C-γ1 (PLCγ1), tSH2-WT, has been used to measure phosphorylation of the epidermal growth factor receptor (EGFR). Here, we found that tSH2-WT lacked specificity for phosphorylated EGFR, consistent with the known promiscuity of SH2 domains. Further, EGF-stimulated membrane recruitment of tSH2-WT differed qualitatively from the expected kinetics of EGFR phosphorylation. Analysis of a mathematical model suggested, and experiments confirmed, that the high avidity of tSH2-WT resulted in saturation of its target and interference with EGFR endocytosis. To overcome the apparent target specificity and saturation issues, we implemented two protein engineering strategies. In the first approach, we screened a combinatorial library generated by random mutagenesis of the C-terminal SH2 domain (cSH2) of PLCγ1 and isolated a mutant form (mSH2) with enhanced specificity for phosphorylated Tyr992 (pTyr992) of EGFR. A biosensor based on mSH2 closely reported the kinetics of EGFR phosphorylation but retained cross-reactivity similar to tSH2-WT. In the second approach, we isolated a pTyr992-binding protein (SPY992) from a combinatorial library generated by mutagenesis of the Sso7d protein scaffold. Compared to tSH2-WT and mSH2, SPY992 exhibited superior performance as a specific, moderate-affinity biosensor. We extended this approach to isolate a biosensor for EGFR pTyr1148 (SPY1148). This approach of integrating theoretical considerations with protein engineering strategies can be generalized to design and evaluate suitable biosensors for various phospho-specific targets.
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Affiliation(s)
- Karthik Tiruthani
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Adam Mischler
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Shoeb Ahmed
- Department of Chemical Engineering, Bangladesh University of Engineering and Technology, Dhaka-1000, Bangladesh
| | - Jessica Mahinthakumar
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Jason M Haugh
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA.
| | - Balaji M Rao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA.
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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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