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Estell C, West S. ZC3H4/Restrictor Exerts a Stranglehold on Pervasive Transcription. J Mol Biol 2024:168707. [PMID: 39002716 DOI: 10.1016/j.jmb.2024.168707] [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: 05/14/2024] [Revised: 07/06/2024] [Accepted: 07/09/2024] [Indexed: 07/15/2024]
Abstract
The regulation of transcription by RNA polymerase II (RNAPII) underpins all cellular processes and is perturbed in thousands of diseases. In humans, RNAPII transcribes ∼20000 protein-coding genes and engages in apparently futile non-coding transcription at thousands of other sites. Despite being so ubiquitous, this transcription is usually attenuated soon after initiation and the resulting products are immediately degraded by the nuclear exosome. We and others have recently described a new complex, "Restrictor", which appears to control such unproductive transcription. Underpinned by the RNA binding protein, ZC3H4, Restrictor curtails unproductive/pervasive transcription genome-wide. Here, we discuss these recent discoveries and speculate on some of the many unknowns regarding Restrictor function and mechanism.
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Affiliation(s)
- Chris Estell
- The Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.
| | - Steven West
- The Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.
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2
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Hermosilla VE, Gyenis L, Rabalski AJ, Armijo ME, Sepúlveda P, Duprat F, Benítez-Riquelme D, Fuentes-Villalobos F, Quiroz A, Hepp MI, Farkas C, Mastel M, González-Chavarría I, Jackstadt R, Litchfield DW, Castro AF, Pincheira R. Casein kinase 2 phosphorylates and induces the SALL2 tumor suppressor degradation in colon cancer cells. Cell Death Dis 2024; 15:223. [PMID: 38493149 PMCID: PMC10944491 DOI: 10.1038/s41419-024-06591-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 02/29/2024] [Accepted: 03/05/2024] [Indexed: 03/18/2024]
Abstract
Spalt-like proteins are Zinc finger transcription factors from Caenorhabditis elegans to vertebrates, with critical roles in development. In vertebrates, four paralogues have been identified (SALL1-4), and SALL2 is the family's most dissimilar member. SALL2 is required during brain and eye development. It is downregulated in cancer and acts as a tumor suppressor, promoting cell cycle arrest and cell death. Despite its critical functions, information about SALL2 regulation is scarce. Public data indicate that SALL2 is ubiquitinated and phosphorylated in several residues along the protein, but the mechanisms, biological consequences, and enzymes responsible for these modifications remain unknown. Bioinformatic analyses identified several putative phosphorylation sites for Casein Kinase II (CK2) located within a highly conserved C-terminal PEST degradation motif of SALL2. CK2 is a serine/threonine kinase that promotes cell proliferation and survival and is often hyperactivated in cancer. We demonstrated that CK2 phosphorylates SALL2 residues S763, T778, S802, and S806 and promotes SALL2 degradation by the proteasome. Accordingly, pharmacological inhibition of CK2 with Silmitasertib (CX-4945) restored endogenous SALL2 protein levels in SALL2-deficient breast MDA-MB-231, lung H1299, and colon SW480 cancer cells. Silmitasertib induced a methuosis-like phenotype and cell death in SW480 cells. However, the phenotype was significantly attenuated in CRISPr/Cas9-mediated SALL2 knockout SW480 cells. Similarly, Sall2-deficient tumor organoids were more resistant to Silmitasertib-induced cell death, confirming that SALL2 sensitizes cancer cells to CK2 inhibition. We identified a novel CK2-dependent mechanism for SALL2 regulation and provided new insights into the interplay between these two proteins and their role in cell survival and proliferation.
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Affiliation(s)
- V E Hermosilla
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Dept of Orofacial Sciences and Dept of Anatomy, University of California-San Francisco, San Francisco, CA, USA
| | - L Gyenis
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada
| | - A J Rabalski
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada
- Odyssey Therapeutics, Boston, MA, USA
| | - M E Armijo
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - P Sepúlveda
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - F Duprat
- Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - D Benítez-Riquelme
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - F Fuentes-Villalobos
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Inmunovirología. Departamento de Microbiologia. Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - A Quiroz
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - M I Hepp
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Investigación en Ciencias Biomédicas, Departamento de Ciencias Básicas y Morfología, Facultad de Medicina, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - C Farkas
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Investigación en Ciencias Biomédicas, Departamento de Ciencias Básicas y Morfología, Facultad de Medicina, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - M Mastel
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg. Cancer Progression and Metastasis Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - I González-Chavarría
- Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - R Jackstadt
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg. Cancer Progression and Metastasis Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - D W Litchfield
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada
| | - A F Castro
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.
| | - R Pincheira
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.
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Bancet A, Frem R, Jeanneret F, Mularoni A, Bazelle P, Roelants C, Delcros JG, Guichou JF, Pillet C, Coste I, Renno T, Battail C, Cochet C, Lomberget T, Filhol O, Krimm I. Cancer selective cell death induction by a bivalent CK2 inhibitor targeting the ATP site and the allosteric αD pocket. iScience 2024; 27:108903. [PMID: 38318383 PMCID: PMC10838953 DOI: 10.1016/j.isci.2024.108903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/25/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
Although the involvement of protein kinase CK2 in cancer is well-documented, there is a need for selective CK2 inhibitors suitable for investigating CK2 specific roles in cancer-related biological pathways and further exploring its therapeutic potential. Here, we report the discovery of AB668, an outstanding selective inhibitor that binds CK2 through a bivalent mode, interacting both at the ATP site and an allosteric αD pocket unique to CK2. Using caspase activation assay, live-cell imaging, and transcriptomic analysis, we have compared the effects of this bivalent inhibitor to representative ATP-competitive inhibitors, CX-4945, and SGC-CK2-1. Our results show that in contrast to CX-4945 or SGC-CK2-1, AB668, by targeting the CK2 αD pocket, has a distinct mechanism of action regarding its anti-cancer activity, inducing apoptotic cell death in several cancer cell lines and stimulating distinct biological pathways in renal cell carcinoma.
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Affiliation(s)
- Alexandre Bancet
- University Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Institut Convergence Plascan, Team « Small Molecules for Biological Targets », 69373 Lyon, France
- Kairos Discovery SAS, 36 Rue Jeanne d’Arc, 69003 Lyon, France
| | - Rita Frem
- University Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Institut Convergence Plascan, Team « Targeting Non-canonical Protein Functions in Cancer », 69373 Lyon, France
| | - Florian Jeanneret
- Université Grenoble Alpes, IRIG, Laboratoire Biosciences et Bioingénierie pour la Santé, UA 13 INSERM-CEA-UGA, 38000 Grenoble, France
| | - Angélique Mularoni
- University Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Institut Convergence Plascan, Team « Small Molecules for Biological Targets », 69373 Lyon, France
| | - Pauline Bazelle
- Université Grenoble Alpes, IRIG, Laboratoire Biosciences et Bioingénierie pour la Santé, UA 13 INSERM-CEA-UGA, 38000 Grenoble, France
| | - Caroline Roelants
- University Grenoble Alpes, INSERM 1292, CEA, UMR Biosanté, 38000 Grenoble, France
| | - Jean-Guy Delcros
- University Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Institut Convergence Plascan, Team « Small Molecules for Biological Targets », 69373 Lyon, France
| | - Jean-François Guichou
- Centre de Biologie Structurale, CNRS, INSERM, University Montpellier, 34090 Montpellier, France
| | - Catherine Pillet
- University Grenoble Alpes, INSERM 1292, CEA, UMR Biosanté, 38000 Grenoble, France
| | - Isabelle Coste
- University Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Institut Convergence Plascan, Team « Targeting Non-canonical Protein Functions in Cancer », 69373 Lyon, France
| | - Toufic Renno
- University Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Institut Convergence Plascan, Team « Targeting Non-canonical Protein Functions in Cancer », 69373 Lyon, France
| | - Christophe Battail
- Université Grenoble Alpes, IRIG, Laboratoire Biosciences et Bioingénierie pour la Santé, UA 13 INSERM-CEA-UGA, 38000 Grenoble, France
| | - Claude Cochet
- University Grenoble Alpes, INSERM 1292, CEA, UMR Biosanté, 38000 Grenoble, France
| | - Thierry Lomberget
- University Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5246, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), COSSBA Team, Faculté de Pharmacie-ISPB, 8 Avenue Rockefeller, 69373 Lyon Cedex 08, France
| | - Odile Filhol
- University Grenoble Alpes, INSERM 1292, CEA, UMR Biosanté, 38000 Grenoble, France
| | - Isabelle Krimm
- University Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Institut Convergence Plascan, Team « Small Molecules for Biological Targets », 69373 Lyon, France
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Choi Y, Yu SR, Lee Y, Na AY, Lee S, Heitman J, Seo R, Lee HS, Lee JS, Bahn YS. Casein kinase 2 complex: a central regulator of multiple pathobiological signaling pathways in Cryptococcus neoformans. mBio 2024; 15:e0327523. [PMID: 38193728 PMCID: PMC10865844 DOI: 10.1128/mbio.03275-23] [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: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 01/10/2024] Open
Abstract
The casein kinase 2 (CK2) complex has garnered extensive attention over the past decades as a potential therapeutic target for diverse human diseases, including cancer, diabetes, and obesity, due to its pivotal roles in eukaryotic growth, differentiation, and metabolic homeostasis. While CK2 is also considered a promising antifungal target, its role in fungal pathogens remains unexplored. In this study, we investigated the functions and regulatory mechanisms of the CK2 complex in Cryptococcus neoformans, a major cause of fungal meningitis. The cryptococcal CK2 complex consists of a single catalytic subunit, Cka1, and two regulatory subunits, Ckb1 and Ckb2. Our findings show that Cka1 plays a primary role as a protein kinase, while Ckb1 and Ckb2 have major and minor regulatory functions, respectively, in growth, cell cycle control, morphogenesis, stress response, antifungal drug resistance, and virulence factor production. Interestingly, triple mutants lacking all three subunits (cka1Δ ckb1Δ ckb2Δ) exhibited more severe phenotypic defects than the cka1Δ mutant alone, suggesting that Ckb1/2 may have Cka1-independent functions. In a murine model of systemic cryptococcosis, cka1Δ and cka1Δ ckb1Δ ckb2Δ mutants showed severely reduced virulence. Transcriptomic, proteomic, and phosphoproteomic analyses further revealed that the CK2 complex controls a wide array of effector proteins involved in transcriptional regulation, cell cycle control, nutrient metabolisms, and stress responses. Most notably, CK2 disruption led to dysregulation of key signaling cascades central to C. neoformans pathogenicity, including the Hog1, Mpk1 MAPKs, cAMP/PKA, and calcium/calcineurin signaling pathways. In summary, our study provides novel insights into the multifaceted roles of the fungal CK2 complex and presents a compelling case for targeting it in the development of new antifungal drugs.IMPORTANCEThe casein kinase 2 (CK2) complex, crucial for eukaryotic growth, differentiation, and metabolic regulation, presents a promising therapeutic target for various human diseases, including cancer, diabetes, and obesity. Its potential as an antifungal target is further highlighted in this study, which explores CK2's functions in C. neoformans, a key fungal meningitis pathogen. The CK2 complex in C. neoformans, comprising the Cka1 catalytic subunit and Ckb1/2 regulatory subunits, is integral to processes like growth, cell cycle, morphogenesis, stress response, drug resistance, and virulence. Our findings of CK2's role in regulating critical signaling pathways, including Hog1, Mpk1 MAPKs, cAMP/PKA, and calcium/calcineurin, underscore its importance in C. neoformans pathogenicity. This study provides valuable insights into the fungal CK2 complex, reinforcing its potential as a target for novel antifungal drug development and pointing out a promising direction for creating new antifungal agents.
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Affiliation(s)
- Yeseul Choi
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Seong-Ryong Yu
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Yujin Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Ann-Yae Na
- School of Pharmacy, Sungkyunkwan University, Suwon, South Korea
| | - Sangkyu Lee
- School of Pharmacy, Sungkyunkwan University, Suwon, South Korea
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Ran Seo
- AmtixBio Co., Ltd., Hanam-si, Gyeonggi-do, South Korea
| | - Han-Seung Lee
- AmtixBio Co., Ltd., Hanam-si, Gyeonggi-do, South Korea
| | | | - Yong-Sun Bahn
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
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Homma MK, Nakato R, Niida A, Bando M, Fujiki K, Yokota N, Yamamoto S, Shibata T, Takagi M, Yamaki J, Kozuka-Hata H, Oyama M, Shirahige K, Homma Y. Cell cycle-dependent gene networks for cell proliferation activated by nuclear CK2α complexes. Life Sci Alliance 2024; 7:e202302077. [PMID: 37907238 PMCID: PMC10618106 DOI: 10.26508/lsa.202302077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 11/02/2023] Open
Abstract
Nuclear expression of protein kinase CK2α is reportedly elevated in human carcinomas, but mechanisms underlying its variable localization in cells are poorly understood. This study demonstrates a functional connection between nuclear CK2 and gene expression in relation to cell proliferation. Growth stimulation of quiescent human normal fibroblasts and phospho-proteomic analysis identified a pool of CK2α that is highly phosphorylated at serine 7. Phosphorylated CK2α translocates into the nucleus, and this phosphorylation appears essential for nuclear localization and catalytic activity. Protein signatures associated with nuclear CK2 complexes reveal enrichment of apparently unique transcription factors and chromatin remodelers during progression through the G1 phase of the cell cycle. Chromatin immunoprecipitation-sequencing profiling demonstrated recruitment of CK2α to active gene loci, more abundantly in late G1 phase than in early G1, notably at transcriptional start sites of core histone genes, growth stimulus-associated genes, and ribosomal RNAs. Our findings reveal that nuclear CK2α complexes may be essential to facilitate progression of the cell cycle, by activating histone genes and triggering ribosomal biogenesis, specified in association with nuclear and nucleolar transcriptional regulators.
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Affiliation(s)
- Miwako Kato Homma
- Department of Biomolecular Sciences, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Ryuichiro Nakato
- Laboratory of Computational Genomics, Institute for Quantitative Biosciences, University of Tokyo, Bunkyo, Japan
| | - Atsushi Niida
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato, Japan
| | - Masashige Bando
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Japan
| | - Katsunori Fujiki
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Japan
| | - Naoko Yokota
- Laboratory of Computational Genomics, Institute for Quantitative Biosciences, University of Tokyo, Bunkyo, Japan
| | - So Yamamoto
- Department of Biomolecular Sciences, Fukushima Medical University School of Medicine, Fukushima, Japan
| | | | - Motoki Takagi
- Translational Research Center, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Junko Yamaki
- Department of Biomolecular Sciences, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Hiroko Kozuka-Hata
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Minato, Japan
| | - Masaaki Oyama
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Minato, Japan
| | - Katsuhiko Shirahige
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Japan
- Department of Biosciences and Nutrition, Karolinska Institutet, Biomedicum, Stockholm, Sweden
- Department of Cell and Molecular Biology, Karolinska Institutet, Biomedicum, Stockholm, Sweden
| | - Yoshimi Homma
- Department of Biomolecular Sciences, Fukushima Medical University School of Medicine, Fukushima, Japan
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Bhat Y, Thrishna MR, Banerjee S. Molecular targets and therapeutic strategies for triple-negative breast cancer. Mol Biol Rep 2023; 50:10535-10577. [PMID: 37924450 DOI: 10.1007/s11033-023-08868-6] [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: 06/23/2023] [Accepted: 09/29/2023] [Indexed: 11/06/2023]
Abstract
Triple-negative breast cancer (TNBC) is known for its heterogeneous complexity and is often difficult to treat. TNBC lacks the expression of major hormonal receptors like estrogen receptor, progesterone receptor, and human epidermal growth factor receptor-2 and is further subdivided into androgen receptor (AR) positive and AR negative. In contrast, AR negative is also known as quadruple-negative breast cancer (QNBC). Compared to AR-positive TNBC, QNBC has a great scarcity of prognostic biomarkers and therapeutic targets. QNBC shows excessive cellular growth and proliferation of tumor cells due to increased expression of growth factors like EGF and various surface proteins. This study briefly reviews the limited data available as protein biomarkers that can be used as molecular targets in treating TNBC as well as QNBC. Targeted therapy and immune checkpoint inhibitors have recently changed cancer treatment. Many studies in medicinal chemistry continue to focus on the synthesis of novel compounds to discover new antiproliferative medicines capable of treating TNBC despite the abundance of treatments currently on the market. Drug repurposing is one of the therapeutic methods for TNBC that has been examined. Moreover, some additional micronutrients, nutraceuticals, and functional foods may be able to lower cancer risk or slow the spread of malignant diseases that have already been diagnosed with cancer. Finally, nanomedicines, or applications of nanotechnology in medicine, introduce nanoparticles with variable chemistry and architecture for the treatment of cancer. This review emphasizes the most recent research on nutraceuticals, medication repositioning, and novel therapeutic strategies for the treatment of TNBC.
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Affiliation(s)
- Yashasvi Bhat
- School of Bio Science and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - M R Thrishna
- School of Bio Science and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Satarupa Banerjee
- School of Bio Science and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India.
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7
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Claridge B, Rai A, Lees JG, Fang H, Lim SY, Greening DW. Cardiomyocyte intercellular signalling increases oxidative stress and reprograms the global- and phospho-proteome of cardiac fibroblasts. JOURNAL OF EXTRACELLULAR BIOLOGY 2023; 2:e125. [PMID: 38938901 PMCID: PMC11080892 DOI: 10.1002/jex2.125] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/20/2023] [Accepted: 11/14/2023] [Indexed: 06/29/2024]
Abstract
Pathological reprogramming of cardiomyocyte and fibroblast proteome landscapes drive the initiation and progression of cardiac fibrosis. Although the secretome of dysfunctional cardiomyocytes is emerging as an important driver of pathological fibroblast reprogramming, our understanding of the downstream molecular players remains limited. Here, we show that cardiac fibroblast activation (αSMA+) and oxidative stress mediated by the secretome of TGFβ-stimulated cardiomyocytes is associated with a profound reprogramming of their proteome and phosphoproteome landscape. Within the fibroblast global proteome there was a striking dysregulation of proteins implicated in extracellular matrix, protein localisation/metabolism, KEAP1-NFE2L2 pathway, lysosomes, carbohydrate metabolism, and transcriptional regulation. Kinase substrate enrichment analysis of phosphopeptides revealed potential role of kinases (CK2, CDK2, PKC, GSK3B) during this remodelling. We verified upregulated activity of casein kinase 2 (CK2) in secretome-treated fibroblasts, and pharmacological CK2 inhibitor TBB (4,5,6,7-Tetrabromobenzotriazole) significantly abrogated fibroblast activation and oxidative stress. Our data provides molecular insights into cardiomyocyte to cardiac fibroblast crosstalk, and the potential role of CK2 in regulating cardiac fibroblast activation and oxidative stress.
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Affiliation(s)
- Bethany Claridge
- Baker Heart and Diabetes InstituteMelbourneVictoriaAustralia
- Baker Department of Cardiovascular Research Translation and ImplementationLa Trobe UniversityMelbourneVictoriaAustralia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and EnvironmentLa Trobe UniversityMelbourneVictoriaAustralia
| | - Alin Rai
- Baker Heart and Diabetes InstituteMelbourneVictoriaAustralia
- Baker Department of Cardiovascular Research Translation and ImplementationLa Trobe UniversityMelbourneVictoriaAustralia
- Baker Department of Cardiometabolic HealthUniversity of MelbourneMelbourneVictoriaAustralia
- Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia
| | - Jarmon G. Lees
- O'Brien Institute DepartmentSt Vincent's Institute of Medical ResearchFitzroyVictoriaAustralia
- Department of Surgery and MedicineUniversity of MelbourneMelbourneVictoriaAustralia
| | - Haoyun Fang
- Baker Heart and Diabetes InstituteMelbourneVictoriaAustralia
- Baker Department of Cardiometabolic HealthUniversity of MelbourneMelbourneVictoriaAustralia
| | - Shiang Y. Lim
- O'Brien Institute DepartmentSt Vincent's Institute of Medical ResearchFitzroyVictoriaAustralia
- Department of Surgery and MedicineUniversity of MelbourneMelbourneVictoriaAustralia
- National Heart Research Institute SingaporeNational Heart CentreSingaporeSingapore
- Drug Discovery Biology, Faculty of Pharmacy and Pharmaceutical SciencesMonash UniversityMelbourneVictoriaAustralia
| | - David W. Greening
- Baker Heart and Diabetes InstituteMelbourneVictoriaAustralia
- Baker Department of Cardiovascular Research Translation and ImplementationLa Trobe UniversityMelbourneVictoriaAustralia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and EnvironmentLa Trobe UniversityMelbourneVictoriaAustralia
- Baker Department of Cardiometabolic HealthUniversity of MelbourneMelbourneVictoriaAustralia
- Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia
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8
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Wippich F, Vaishali, Hennrich ML, Ephrussi A. Nutritional stress-induced regulation of microtubule organization and mRNP transport by HDAC1 controlled α-tubulin acetylation. Commun Biol 2023; 6:776. [PMID: 37491525 PMCID: PMC10368696 DOI: 10.1038/s42003-023-05138-w] [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: 10/14/2020] [Accepted: 07/12/2023] [Indexed: 07/27/2023] Open
Abstract
In response to nutritional stress, microtubules in cells of the Drosophila female germline are depleted from the cytoplasm and accumulate cortically. This triggers aggregation of mRNPs into large processing bodies (P-bodies) and oogenesis arrest. Here, we show that hyperacetylation of α-tubulin at lysine 40 (K40) alters microtubule dynamics and P-body formation. We found that depletion of histone deacetylase 1 (HDAC1) by RNAi phenocopies the nutritional stress response, causing α-tubulin hyperacetylation and accumulation of maternally deposited mRNPs in P-bodies. Through in vitro and in vivo studies, we identify HDAC1 as a direct regulator of α-tubulin K40 acetylation status. In well-fed flies, HDAC1 maintains low levels of α-tubulin acetylation, enabling the microtubule dynamics required for mRNP transport. Using quantitative phosphoproteomics we identify nutritional stress-induced changes in protein phosphorylation that act upstream of α-tubulin acetylation, including phosphorylation of HDAC1 at S391, which reduces its ability to deacetylate α-tubulin. These results reveal that Drosophila HDAC1 senses and relays the nutritional status, which regulates germline development through modulation of cytoskeleton dynamics.
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Affiliation(s)
- Frank Wippich
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, Heidelberg, 69117, Germany
- Cellzome GmbH, GlaxoSmithKline, Heidelberg, Germany
| | - Vaishali
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, Heidelberg, 69117, Germany
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Marco L Hennrich
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, Heidelberg, 69117, Germany
- Cellzome GmbH, GlaxoSmithKline, Heidelberg, Germany
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, Heidelberg, 69117, Germany.
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9
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Patel S, Vyas VK, Sharma M, Ghate M. Structure-guided discovery of adenosine triphosphate-competitive casein kinase 2 inhibitors. Future Med Chem 2023; 15:987-1014. [PMID: 37307219 DOI: 10.4155/fmc-2023-0005] [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] [Indexed: 06/14/2023] Open
Abstract
Casein kinase 2 (CK2) is a ubiquitous, highly pleiotropic serine-threonine kinase. CK2 has been identified as a potential drug target for the treatment of cancer and related disorders. Several adenosine triphosphate-competitive CK2 inhibitors have been identified and have progressed at different levels of clinical trials. This review presents details of CK2 protein, structural insights into adenosine triphosphate binding pocket, current clinical trial candidates and their analogues. Further, it includes the emerging structure-based drug design approaches, chemistry, structure-activity relationship and biological screening of potent and selective CK2 inhibitors. The authors tabulated the details of CK2 co-crystal structures because these co-crystal structures facilitated the structure-guided discovery of CK2 inhibitors. The narrow hinge pocket compared with related kinases provides useful insights into the discovery of CK2 inhibitors.
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Affiliation(s)
- Shivani Patel
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India
| | - Vivek K Vyas
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India
| | - Manmohan Sharma
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India
| | - Manjunath Ghate
- School of Pharmacy, National Forensic Science University, Gandhinagar, Gujarat, 382007, India
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10
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Nickelsen A, Götz C, Lenz F, Niefind K, König S, Jose J. Analyzing the interactome of human CK2β in prostate carcinoma cells reveals HSP70-1 and Rho guanin nucleotide exchange factor 12 as novel interaction partners. FASEB Bioadv 2023; 5:114-130. [PMID: 36876296 PMCID: PMC9983076 DOI: 10.1096/fba.2022-00098] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/19/2022] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
CK2β is the non-catalytic modulating part of the S/T-protein kinase CK2. However, the overall function of CK2β is poorly understood. Here, we report on the identification of 38 new interaction partners of the human CK2β from lysates of DU145 prostate cancer cells using photo-crosslinking and mass spectrometry, whereby HSP70-1 was identified with high abundance. The KD value of its interaction with CK2β was determined as 0.57 μM by microscale thermophoresis, this being the first time, to our knowledge, that a KD value of CK2β with another protein than CK2α or CK2α' was quantified. Phosphorylation studies excluded HSP70-1 as a substrate or activity modulator of CK2, suggesting a CK2 activity independent interaction of HSP70-1 with CK2β. Co-immunoprecipitation experiments in three different cancer cell lines confirmed the interaction of HSP70-1 with CK2β in vivo. A second identified CK2β interaction partner was Rho guanin nucleotide exchange factor 12, indicating an involvement of CK2β in the Rho-GTPase signal pathway, described here for the first time to our knowledge. This points to a role of CK2β in the interaction network affecting the organization of the cytoskeleton.
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Affiliation(s)
- Anna Nickelsen
- Institute of Pharmaceutical and Medicinal Chemistry University of Münster Münster Germany
| | - Claudia Götz
- Department of Medical Biochemistry and Molecular Biology Saarland University Homburg Germany
| | - Florian Lenz
- Institute of Pharmaceutical and Medicinal Chemistry University of Münster Münster Germany
| | - Karsten Niefind
- Department of Chemistry, Institute of Biochemistry University of Cologne Köln Germany
| | - Simone König
- Interdisciplinary Center for Clinical Research, Core Unit Proteomics, Medical Faculty University of Münster Münster Germany
| | - Joachim Jose
- Institute of Pharmaceutical and Medicinal Chemistry University of Münster Münster Germany
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11
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Minor Kinases with Major Roles in Cytokinesis Regulation. Cells 2022; 11:cells11223639. [PMID: 36429067 PMCID: PMC9688779 DOI: 10.3390/cells11223639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/07/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
Cytokinesis, the conclusive act of cell division, allows cytoplasmic organelles and chromosomes to be faithfully partitioned between two daughter cells. In animal organisms, its accurate regulation is a fundamental task for normal development and for preventing aneuploidy. Cytokinesis failures produce genetically unstable tetraploid cells and ultimately result in chromosome instability, a hallmark of cancer cells. In animal cells, the assembly and constriction of an actomyosin ring drive cleavage furrow ingression, resulting in the formation of a cytoplasmic intercellular bridge, which is severed during abscission, the final event of cytokinesis. Kinase-mediated phosphorylation is a crucial process to orchestrate the spatio-temporal regulation of the different stages of cytokinesis. Several kinases have been described in the literature, such as cyclin-dependent kinase, polo-like kinase 1, and Aurora B, regulating both furrow ingression and/or abscission. However, others exist, with well-established roles in cell-cycle progression but whose specific role in cytokinesis has been poorly investigated, leading to considering these kinases as "minor" actors in this process. Yet, they deserve additional attention, as they might disclose unexpected routes of cell division regulation. Here, we summarize the role of multifunctional kinases in cytokinesis with a special focus on those with a still scarcely defined function during cell cleavage. Moreover, we discuss their implication in cancer.
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12
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Okanishi H, Ohgaki R, Xu M, Endou H, Kanai Y. Phosphoproteomics revealed cellular signals immediately responding to disruption of cancer amino acid homeostasis induced by inhibition of l-type amino acid transporter 1. Cancer Metab 2022; 10:18. [PMID: 36357940 PMCID: PMC9650822 DOI: 10.1186/s40170-022-00295-8] [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: 08/02/2022] [Accepted: 10/26/2022] [Indexed: 11/12/2022] Open
Abstract
Background Cancer-upregulated l-type amino acid transporter 1 (LAT1; SLC7A5) supplies essential amino acids to cancer cells. LAT1 substrates are not only needed for cancer rapid growth, but involved in cellular signaling. LAT1 has been proposed as a potential target for cancer treatment—its inhibitor, JPH203, is currently in clinical trials and targets biliary tract cancer (BTC). Here, we revealed to what extent LAT1 inhibitor affects intracellular amino acid content and what kind of cellular signals are directly triggered by LAT1 inhibition. Methods Liquid chromatography assay combined with o-phthalaldehyde- and 9-fluorenyl-methylchloroformate-based derivatization revealed changes in intracellular amino acid levels induced by LAT1 inhibition with JPH203 treatment in three BTC cell lines. Tandem mass tag-based quantitative phosphoproteomics characterized the effect of JPH203 treatment on BTC cells, and suggested key regulators in LAT1-inhibited cells. We further studied one of the key regulators, CK2 protein kinase, by using Western blot, enzymatic activity assay, and co-immunoprecipitation. We evaluated anticancer effects of combination of JPH203 with CK2 inhibitor using cell growth and would healing assay. Results JPH203 treatment decreased intracellular levels of LAT1 substrates including essential amino acids of three BTC cell lines, immediately and drastically. We also found levels of some of these amino acids were partially recovered after longer-time treatment. Therefore, we performed phosphoproteomics with short-time JPH203 treatment prior to the cellular compensatory response, and revealed hundreds of differentially phosphorylated sites. Commonly downregulated phosphorylation sites were found on proteins involved in the cell cycle and RNA splicing. Our phosphoproteomics also suggested key regulators immediately responding to LAT1 inhibition. Focusing on one of these regulators, protein kinase CK2, we revealed LAT1 inhibition decreased phosphorylation of CK2 substrate without changing CK2 enzymatic activity. Furthermore, LAT1 inhibition abolished interaction between CK2 and its regulatory protein NOLC1, which suggests regulatory mechanism of CK2 substrate protein specificity controlled by LAT1 inhibition. Moreover, we revealed that the combination of JPH203 with CK2 inhibitor resulted in the enhanced inhibition of proliferation and migration of BTC cells. Conclusion This study provides new perspectives on LAT1-dependent cellular processes and a rationale for therapeutics targeting reprogrammed cancer metabolism. Supplementary Information The online version contains supplementary material available at 10.1186/s40170-022-00295-8.
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13
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Trembley JH, Kren BT, Afzal M, Scaria GA, Klein MA, Ahmed K. Protein kinase CK2 – diverse roles in cancer cell biology and therapeutic promise. Mol Cell Biochem 2022; 478:899-926. [PMID: 36114992 PMCID: PMC9483426 DOI: 10.1007/s11010-022-04558-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/01/2022] [Indexed: 11/29/2022]
Abstract
The association of protein kinase CK2 (formerly casein kinase II or 2) with cell growth and proliferation in cells was apparent at early stages of its investigation. A cancer-specific role for CK2 remained unclear until it was determined that CK2 was also a potent suppressor of cell death (apoptosis); the latter characteristic differentiated its function in normal versus malignant cells because dysregulation of both cell growth and cell death is a universal feature of cancer cells. Over time, it became evident that CK2 exerts its influence on a diverse range of cell functions in normal as well as in transformed cells. As such, CK2 and its substrates are localized in various compartments of the cell. The dysregulation of CK2 is documented in a wide range of malignancies; notably, by increased CK2 protein and activity levels with relatively moderate change in its RNA abundance. High levels of CK2 are associated with poor prognosis in multiple cancer types, and CK2 is a target for active research and testing for cancer therapy. Aspects of CK2 cellular roles and targeting in cancer are discussed in the present review, with focus on nuclear and mitochondrial functions and prostate, breast and head and neck malignancies.
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Affiliation(s)
- Janeen H Trembley
- Research Service, Minneapolis VA Health Care System, Minneapolis, MN, 55417, USA.
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, 55455, USA.
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Betsy T Kren
- Research Service, Minneapolis VA Health Care System, Minneapolis, MN, 55417, USA
| | - Muhammad Afzal
- Department of Biochemistry, Riphah International University, Islamabad, Pakistan
| | - George A Scaria
- Hematology/Oncology Section, Primary Care Service Line, Minneapolis VA Health Care System, Minneapolis, MN, 55417, USA
| | - Mark A Klein
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
- Hematology/Oncology Section, Primary Care Service Line, Minneapolis VA Health Care System, Minneapolis, MN, 55417, USA
- Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Khalil Ahmed
- Research Service, Minneapolis VA Health Care System, Minneapolis, MN, 55417, USA.
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, 55455, USA.
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA.
- Department of Urology, University of Minnesota, Minneapolis, MN, 55455, USA.
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14
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White A, McGlone A, Gomez-Pastor R. Protein Kinase CK2 and Its Potential Role as a Therapeutic Target in Huntington's Disease. Biomedicines 2022; 10:1979. [PMID: 36009526 PMCID: PMC9406209 DOI: 10.3390/biomedicines10081979] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
Huntington's Disease (HD) is a devastating neurodegenerative disorder caused by a CAG trinucleotide repeat expansion in the HTT gene, for which no disease modifying therapies are currently available. Much of the recent research has focused on developing therapies to directly lower HTT expression, and while promising, these therapies have presented several challenges regarding administration and efficacy. Another promising therapeutic approach is the modulation of HTT post-translational modifications (PTMs) that are dysregulated in disease and have shown to play a key role in HTT toxicity. Among all PTMs, modulation of HTT phosphorylation has been proposed as an attractive therapeutic option due to the possibility of orally administering specific kinase effectors. One of the kinases described to participate in HTT phosphorylation is Protein Kinase CK2. CK2 has recently emerged as a target for the treatment of several neurological and psychiatric disorders, although its role in HD remains controversial. While pharmacological studies in vitro inhibiting CK2 resulted in reduced HTT phosphorylation and increased toxicity, genetic approaches in mouse models of HD have provided beneficial effects. In this review we discuss potential therapeutic approaches related to the manipulation of HTT-PTMs with special emphasis on the role of CK2 as a therapeutic target in HD.
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Affiliation(s)
| | | | - Rocio Gomez-Pastor
- Department of Neuroscience, School of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
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15
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Asif M, Kaygusuz E, Shinawi M, Nickelsen A, Hsieh TC, Wagle P, Budde BS, Hochscherf J, Abdullah U, Höning S, Nienberg C, Lindenblatt D, Noegel AA, Altmüller J, Thiele H, Motameny S, Fleischer N, Segal I, Pais L, Tinschert S, Samra NN, Savatt JM, Rudy NL, De Luca C, Paola Fortugno, White SM, Krawitz P, Hurst ACE, Niefind K, Jose J, Brancati F, Nürnberg P, Hussain MS. De novo variants of CSNK2B cause a new intellectual disability-craniodigital syndrome by disrupting the canonical Wnt signaling pathway. HGG ADVANCES 2022; 3:100111. [PMID: 35571680 PMCID: PMC9092267 DOI: 10.1016/j.xhgg.2022.100111] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/13/2022] [Indexed: 11/29/2022] Open
Abstract
CSNK2B encodes for casein kinase II subunit beta (CK2β), the regulatory subunit of casein kinase II (CK2), which is known to mediate diverse cellular pathways. Variants in this gene have been recently identified as a cause of Poirier-Bienvenu neurodevelopmental syndrome (POBINDS), but functional evidence is sparse. Here, we report five unrelated individuals: two of them manifesting POBINDS, while three are identified to segregate a new intellectual disability-craniodigital syndrome (IDCS), distinct from POBINDS. The three IDCS individuals carried two different de novo missense variants affecting the same codon of CSNK2B. Both variants, NP_001311.3; p.Asp32His and NP_001311.3; p.Asp32Asn, lead to an upregulation of CSNK2B expression at transcript and protein level, along with global dysregulation of canonical Wnt signaling. We found impaired interaction of the two key players DVL3 and β-catenin with mutated CK2β. The variants compromise the kinase activity of CK2 as evident by a marked reduction of phosphorylated β-catenin and consequent absence of active β-catenin inside nuclei of the patient-derived lymphoblastoid cell lines (LCLs). In line with these findings, whole-transcriptome profiling of patient-derived LCLs harboring the NP_001311.3; p.Asp32His variant confirmed a marked difference in expression of genes involved in the Wnt signaling pathway. In addition, whole-phosphoproteome analysis of the LCLs of the same subject showed absence of phosphorylation for 313 putative CK2 substrates, enriched in the regulation of nuclear β-catenin and transcription of the target genes. Our findings suggest that discrete variants in CSNK2B cause dominant-negative perturbation of the canonical Wnt signaling pathway, leading to a new craniodigital syndrome distinguishable from POBINDS.
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Affiliation(s)
- Maria Asif
- Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany.,Center for Biochemistry, Medical Faculty, University of Cologne, 50931 Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
| | - Emrah Kaygusuz
- Center for Biochemistry, Medical Faculty, University of Cologne, 50931 Cologne, Germany.,Bilecik Şeyh Edebali University, Molecular Biology and Genetics, Gülümbe Campus, 11230 Bilecik, Turkey
| | - Marwan Shinawi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Anna Nickelsen
- Institute of Pharmaceutical and Medicinal Chemistry, Westphalian Wilhelms-University, Münster, Germany
| | - Tzung-Chien Hsieh
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich Wilhelms, Universität Bonn, Bonn, Germany
| | - Prerana Wagle
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Birgit S Budde
- Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
| | - Jennifer Hochscherf
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Uzma Abdullah
- University Institute of Biochemistry and Biotechnology (UIBB), PMAS-Arid Agriculture University, Rawalpindi, Pakistan
| | - Stefan Höning
- Center for Biochemistry, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Christian Nienberg
- Institute of Pharmaceutical and Medicinal Chemistry, Westphalian Wilhelms-University, Münster, Germany
| | - Dirk Lindenblatt
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Angelika A Noegel
- Center for Biochemistry, Medical Faculty, University of Cologne, 50931 Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany.,Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Facility Genomics, Charitéplatz 1, 10117 Berlin, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
| | - Susanne Motameny
- Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
| | | | | | - Lynn Pais
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sigrid Tinschert
- Zentrum Medizinische Genetik, Medizinische Universität, Innsbruck, Austria
| | - Nadra Nasser Samra
- Hospital Center, Safed, Israel.,Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | | | - Natasha L Rudy
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Chiara De Luca
- Department of Life, Health and Environmental Science, University of L'Aquila, 67100 L'Aquila, Italy
| | | | - Paola Fortugno
- Department of Life, Health and Environmental Science, University of L'Aquila, 67100 L'Aquila, Italy.,IRCCS, San Raffaele Roma, 00163 Roma, Italy
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich Wilhelms, Universität Bonn, Bonn, Germany
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Karsten Niefind
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Joachim Jose
- Institute of Pharmaceutical and Medicinal Chemistry, Westphalian Wilhelms-University, Münster, Germany
| | - Francesco Brancati
- Department of Life, Health and Environmental Science, University of L'Aquila, 67100 L'Aquila, Italy.,IRCCS, San Raffaele Roma, 00163 Roma, Italy
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
| | - Muhammad Sajid Hussain
- Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany.,Center for Biochemistry, Medical Faculty, University of Cologne, 50931 Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
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16
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Yu D, Zarate N, White A, Coates D, Tsai W, Nanclares C, Cuccu F, Yue JS, Brown TG, Mansky RH, Jiang K, Kim H, Nichols-Meade T, Larson SN, Gundry K, Zhang Y, Tomas-Zapico C, Lucas JJ, Benneyworth M, Öz G, Cvetanovic M, Araque A, Gomez-Pastor R. CK2 alpha prime and alpha-synuclein pathogenic functional interaction mediates synaptic dysregulation in huntington's disease. Acta Neuropathol Commun 2022; 10:83. [PMID: 35659303 PMCID: PMC9164558 DOI: 10.1186/s40478-022-01379-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/05/2022] [Indexed: 12/26/2022] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by a CAG trinucleotide repeat expansion in the HTT gene for which no therapies are available. HTT mutation causes protein misfolding and aggregation, preferentially affecting medium spiny neurons (MSNs) of the basal ganglia. Transcriptional perturbations in synaptic genes and neuroinflammation are key processes that precede MSN dysfunction and motor symptom onset. Understanding the interplay between these processes is crucial to develop effective therapeutic strategies to treat HD. We investigated the role of protein kinase CK2α', a kinase upregulated in MSNs in HD and previously associated with Parkinson's disease (PD), in the regulation of neuroinflammation and synaptic function in HD. We used the heterozygous knock-in zQ175 HD mouse model and compared that to zQ175 mice lacking one allele of CK2α' (zQ175:CK2α'(±)). CK2α' haploinsufficiency in zQ175 mice resulted in decreased levels of pro-inflammatory cytokines, HTT aggregation, astrogliosis and transcriptional alterations of synaptic genes related to glutamatergic signaling. zQ175:CK2α'(±) mice also presented increased frequency of striatal miniature excitatory postsynaptic currents (mEPSCs), an indicator of synaptic activity, and improved motor coordination compared to zQ175 mice. Neuropathological and phenotypic changes mediated by CK2α' were connected to alpha-synuclein (α-syn) dysregulation and correlated with differences in α-syn serine 129 phosphorylation (pS129-α-syn), a post-translational modification involved in α-synucleinopathy and shown to be regulated by CK2 in PD. pS129-α-syn was increased in the nuclei of MSNs in zQ175 mice and in the striatum of patients with HD, and it decreased in zQ175:CK2α'(±) mice. Collectively, our data established a novel connection between CK2α', neuroinflammation and synaptic gene dysregulation with synucleinopathy in HD and suggested common molecular mechanisms of neurodegeneration between HD and PD. Our results also support CK2α' inhibition as a potential therapeutic strategy to modulate neuronal function and neuroprotection in HD.
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Affiliation(s)
- Dahyun Yu
- Department of Neuroscience, School of Medicine, University of Minnesota, 321 Church St. SE, Jackson Hall Room 6-145, Minneapolis, MN USA
| | - Nicole Zarate
- Department of Neuroscience, School of Medicine, University of Minnesota, 321 Church St. SE, Jackson Hall Room 6-145, Minneapolis, MN USA
| | - Angel White
- Department of Neuroscience, School of Medicine, University of Minnesota, 321 Church St. SE, Jackson Hall Room 6-145, Minneapolis, MN USA
| | - De’jah Coates
- Department of Neuroscience, School of Medicine, University of Minnesota, 321 Church St. SE, Jackson Hall Room 6-145, Minneapolis, MN USA
| | - Wei Tsai
- Department of Neuroscience, School of Medicine, University of Minnesota, 321 Church St. SE, Jackson Hall Room 6-145, Minneapolis, MN USA
| | - Carmen Nanclares
- Department of Neuroscience, School of Medicine, University of Minnesota, 321 Church St. SE, Jackson Hall Room 6-145, Minneapolis, MN USA
| | - Francesco Cuccu
- Department of Neuroscience, School of Medicine, University of Minnesota, 321 Church St. SE, Jackson Hall Room 6-145, Minneapolis, MN USA
- Department of Life and Environment Sciences, University of Cagliari, Cagliari, Italy
| | - Johnny S. Yue
- Department of Neuroscience, School of Medicine, University of Minnesota, 321 Church St. SE, Jackson Hall Room 6-145, Minneapolis, MN USA
- Mounds View High School, Arden Hills, MN USA
| | - Taylor G. Brown
- Department of Neuroscience, School of Medicine, University of Minnesota, 321 Church St. SE, Jackson Hall Room 6-145, Minneapolis, MN USA
| | - Rachel H. Mansky
- Department of Neuroscience, School of Medicine, University of Minnesota, 321 Church St. SE, Jackson Hall Room 6-145, Minneapolis, MN USA
| | - Kevin Jiang
- Department of Neuroscience, School of Medicine, University of Minnesota, 321 Church St. SE, Jackson Hall Room 6-145, Minneapolis, MN USA
| | - Hyuck Kim
- Department of Neuroscience, School of Medicine, University of Minnesota, 321 Church St. SE, Jackson Hall Room 6-145, Minneapolis, MN USA
- Present Address: HK, MEPSGEN, Seoul, 05836 South Korea
- Present Address: CTZ Department of Functional Biology, Physiology, University of Oviedo, 33006 Asturias, Spain
- Present Address: Health Research Institute of the Principality of Asturias (ISPA), 33011 Asturias, Spain
| | - Tessa Nichols-Meade
- Department of Neuroscience, School of Medicine, University of Minnesota, 321 Church St. SE, Jackson Hall Room 6-145, Minneapolis, MN USA
| | - Sarah N. Larson
- Center for Magnetic Resonance Research. Department of Radiology, School of Medicine, University of Minnesota, Minneapolis, MN USA
| | - Katherine Gundry
- Center for Magnetic Resonance Research. Department of Radiology, School of Medicine, University of Minnesota, Minneapolis, MN USA
| | - Ying Zhang
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN USA
| | - Cristina Tomas-Zapico
- Centro de Biología Molecular ‘Severo Ochoa’ (CBMSO) CSIC/UAM, Madrid, Spain
- Present Address: HK, MEPSGEN, Seoul, 05836 South Korea
- Present Address: CTZ Department of Functional Biology, Physiology, University of Oviedo, 33006 Asturias, Spain
- Present Address: Health Research Institute of the Principality of Asturias (ISPA), 33011 Asturias, Spain
| | - Jose J. Lucas
- Centro de Biología Molecular ‘Severo Ochoa’ (CBMSO) CSIC/UAM, Madrid, Spain
- Networking Research Center On Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Michael Benneyworth
- Department of Neuroscience, School of Medicine, University of Minnesota, 321 Church St. SE, Jackson Hall Room 6-145, Minneapolis, MN USA
| | - Gülin Öz
- Center for Magnetic Resonance Research. Department of Radiology, School of Medicine, University of Minnesota, Minneapolis, MN USA
| | - Marija Cvetanovic
- Department of Neuroscience, School of Medicine, University of Minnesota, 321 Church St. SE, Jackson Hall Room 6-145, Minneapolis, MN USA
| | - Alfonso Araque
- Department of Neuroscience, School of Medicine, University of Minnesota, 321 Church St. SE, Jackson Hall Room 6-145, Minneapolis, MN USA
| | - Rocio Gomez-Pastor
- Department of Neuroscience, School of Medicine, University of Minnesota, 321 Church St. SE, Jackson Hall Room 6-145, Minneapolis, MN USA
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17
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Schwein PA, Ge Y, Yang B, D’Souza A, Mody A, Shen D, Woo CM. Writing and Erasing O-GlcNAc on Casein Kinase 2 Alpha Alters the Phosphoproteome. ACS Chem Biol 2022; 17:1111-1121. [PMID: 35467332 DOI: 10.1021/acschembio.1c00987] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
O-GlcNAc is an essential carbohydrate modification that intersects with phosphorylation signaling pathways via crosstalk on protein substrates or by direct modification of the kinases that write the phosphate modification. Casein kinase 2 alpha (CK2α), the catalytic subunit of the ubiquitously expressed and constitutively active kinase CK2, is modified by O-GlcNAc, but the effect of this modification on the phosphoproteome in cells is unknown. Here, we apply complementary targeted O-GlcNAc editors, nanobody-OGT and -splitOGA, to selectively write and erase O-GlcNAc from a tagged CK2α to measure the effects on the phosphoproteome in cells. These tools effectively and selectively edit the Ser347 glycosite on CK2α. Using quantitative phosphoproteomics, we report 51 phosphoproteins whose enrichment changes as a function of editing O-GlcNAc on CK2α, including HDAC1, HDAC2, ENSA, SMARCAD1, and PABPN1. Specific phosphosites on HDAC1 Ser393 and HDAC2 Ser394, both reported CK2 substrates, are significantly enhanced by O-GlcNAcylation of CK2α. These data will propel future studies on the crosstalk between O-GlcNAc and phosphorylation.
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Affiliation(s)
- Paul A. Schwein
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| | - Yun Ge
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| | - Bo Yang
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| | - Alexandria D’Souza
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| | - Alison Mody
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| | - Dacheng Shen
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| | - Christina M. Woo
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
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18
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Park K, Zhong J, Jang JS, Kim J, Kim HJ, Lee JH, Kim J. ZWC complex-mediated SPT5 phosphorylation suppresses divergent antisense RNA transcription at active gene promoters. Nucleic Acids Res 2022; 50:3835-3851. [PMID: 35325203 PMCID: PMC9023261 DOI: 10.1093/nar/gkac193] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/08/2022] [Accepted: 03/13/2022] [Indexed: 11/14/2022] Open
Abstract
The human genome encodes large numbers of non-coding RNAs, including divergent antisense transcripts at transcription start sites (TSSs). However, molecular mechanisms by which divergent antisense transcription is regulated have not been detailed. Here, we report a novel ZWC complex composed of ZC3H4, WDR82 and CK2 that suppresses divergent antisense transcription. The ZWC complex preferentially localizes at TSSs of active genes through direct interactions of ZC3H4 and WDR82 subunits with the S5p RNAPII C-terminal domain. ZC3H4 depletion leads to increased divergent antisense transcription, especially at genes that naturally produce divergent antisense transcripts. We further demonstrate that the ZWC complex phosphorylates the previously uncharacterized N-terminal acidic domain of SPT5, a subunit of the transcription-elongation factor DSIF, and that this phosphorylation is responsible for suppressing divergent antisense transcription. Our study provides evidence that the newly identified ZWC-DSIF axis regulates the direction of transcription during the transition from early to productive elongation.
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Affiliation(s)
- Kihyun Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Jian Zhong
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Jin Sung Jang
- Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jihyun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Hye-Jung Kim
- New Drug Development Center, OSONG Medical Innovation Foundation, Cheongju 28160, South Korea
| | - Jeong-Heon Lee
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
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19
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Ulreich K, Firnau MB, Tagscherer N, Beyer S, Ackermann A, Plotz G, Brieger A. High Expression of Casein Kinase 2 Alpha Is Responsible for Enhanced Phosphorylation of DNA Mismatch Repair Protein MLH1 and Increased Tumor Mutation Rates in Colorectal Cancer. Cancers (Basel) 2022; 14:cancers14061553. [PMID: 35326704 PMCID: PMC8946085 DOI: 10.3390/cancers14061553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/10/2022] [Accepted: 03/15/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Colorectal cancer (CRC) is associated with DNA mismatch repair (MMR) deficiency. The serine/threonine casein kinase 2 alpha (CK2α) is able to phosphorylate and inhibit MMR protein MLH1 in vitro. This study aimed to analyze the relevance of CK2α for MLH1 phosphorylation in vivo. Around 50% of CRCs were identified to express significantly increased nuclear/cytoplasmic CK2α. High nuclear/cytoplasmic CK2α level could be significantly correlated with reduced 5-year survival outcome of patients, increased MLH1 phosphorylation, and enriched somatic tumor mutation rates. Overall, our study demonstrated, in vivo, that enhanced CK2α leads to an increase of MLH1 phosphorylation, higher tumor mutation rates, and is an unfavorable prognosis for patients. Abstract DNA mismatch repair (MMR) deficiency plays an essential role in the development of colorectal cancer (CRC). We recently demonstrated in vitro that the serine/threonine casein kinase 2 alpha (CK2α) causes phosphorylation of the MMR protein MLH1 at position serine 477, which significantly inhibits the MMR. In the present study, CK2α-dependent MLH1 phosphorylation was analyzed in vivo. Using a cohort of 165 patients, we identified 88 CRCs showing significantly increased nuclear/cytoplasmic CK2α expression, 28 tumors with high nuclear CK2α expression and 49 cases showing a general low CK2α expression. Patients with high nuclear/cytoplasmic CK2α expression demonstrated significantly reduced 5-year survival outcome. By immunoprecipitation and Western blot analysis, we showed that high nuclear/cytoplasmic CK2α expression significantly correlates with increased MLH1 phosphorylation and enriched somatic tumor mutation rates. The CK2α mRNA levels tended to be enhanced in high nuclear/cytoplasmic and high nuclear CK2α-expressing tumors. Furthermore, we identified various SNPs in the promotor region of CK2α, which might cause differential CK2α expression. In summary, we demonstrated that high nuclear/cytoplasmic CK2α expression in CRCs correlates with enhanced MLH1 phosphorylation in vivo and seems to be causative for increased mutation rates, presumably induced by reduced MMR. These observations could provide important new therapeutic targets.
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20
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BRCA1 mutations in high-grade serous ovarian cancer are associated with proteomic changes in DNA repair, splicing, transcription regulation and signaling. Sci Rep 2022; 12:4445. [PMID: 35292711 PMCID: PMC8924168 DOI: 10.1038/s41598-022-08461-0] [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: 05/10/2021] [Accepted: 02/23/2022] [Indexed: 11/08/2022] Open
Abstract
Despite recent advances in the management of BRCA1 mutated high-grade serous ovarian cancer (HGSC), the physiology of these tumors remains poorly understood. Here we provide a comprehensive molecular understanding of the signaling processes that drive HGSC pathogenesis with the addition of valuable ubiquitination profiling, and their dependency on BRCA1 mutation-state directly in patient-derived tissues. Using a multilayered proteomic approach, we show the tight coordination between the ubiquitination and phosphorylation regulatory layers and their role in key cellular processes related to BRCA1-dependent HGSC pathogenesis. In addition, we identify key bridging proteins, kinase activity, and post-translational modifications responsible for molding distinct cancer phenotypes, thus providing new opportunities for therapeutic intervention, and ultimately advance towards a more personalized patient care.
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21
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Ramón AC, Pérez GV, Caballero E, Rosales M, Aguilar D, Vázquez-Blomquist D, Ramos Y, Rodríguez-Ulloa A, Falcón V, Rodríguez-Moltó MP, Yang K, Perera Y, Perea SE. Targeting of Protein Kinase CK2 Elicits Antiviral Activity on Bovine Coronavirus Infection. Viruses 2022; 14:552. [PMID: 35336959 PMCID: PMC8949182 DOI: 10.3390/v14030552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/07/2022] Open
Abstract
Coronaviruses constitute a global threat to the human population; therefore, effective pan-coronavirus antiviral drugs are required to tackle future re-emerging virus outbreaks. Protein kinase CK2 has been suggested as a promising therapeutic target in COVID-19 owing to the in vitro antiviral activity observed after both pharmacologic and genetic inhibition of the enzyme. Here, we explored the putative antiviral effect of the anti-CK2 peptide CIGB-325 on bovine coronavirus (BCoV) infection using different in vitro viral infected cell-based assays. The impact of the peptide on viral mRNA and protein levels was determined by qRT-PCR and Western blot, respectively. Finally, pull-down experiments followed by Western blot and/or mass spectrometry analysis were performed to identify CIGB-325-interacting proteins. We found that CIGB-325 inhibited both the cytopathic effect and the number of plaque-forming units. Accordingly, intracellular viral protein levels were clearly reduced after treatment of BCoV-infected cells, with CIGB-325 determined by immunocytochemistry. Pull-down assay data revealed the physical interaction of CIGB-325 with viral nucleocapsid (N) protein and a group of bona fide CK2 cellular substrates. Our findings evidence in vitro antiviral activity of CIGB-325 against bovine coronavirus as well as some molecular clues that might support such effect. Altogether, data provided here strengthen the rationale of inhibiting CK2 to treat betacoronavirus infections.
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Affiliation(s)
- Ailyn C. Ramón
- Molecular Oncology Group, Department of Pharmaceuticals, Biomedical Research Division, Center for Genetic Engineering and Biotechnology, Havana 10600, Cuba; (A.C.R.); (G.V.P.); (E.C.); (M.R.); (D.A.)
| | - George V. Pérez
- Molecular Oncology Group, Department of Pharmaceuticals, Biomedical Research Division, Center for Genetic Engineering and Biotechnology, Havana 10600, Cuba; (A.C.R.); (G.V.P.); (E.C.); (M.R.); (D.A.)
| | - Evelin Caballero
- Molecular Oncology Group, Department of Pharmaceuticals, Biomedical Research Division, Center for Genetic Engineering and Biotechnology, Havana 10600, Cuba; (A.C.R.); (G.V.P.); (E.C.); (M.R.); (D.A.)
| | - Mauro Rosales
- Molecular Oncology Group, Department of Pharmaceuticals, Biomedical Research Division, Center for Genetic Engineering and Biotechnology, Havana 10600, Cuba; (A.C.R.); (G.V.P.); (E.C.); (M.R.); (D.A.)
- Department of Animal and Human Biology, Faculty of Biology, University of Havana, Havana 10400, Cuba
| | - Daylén Aguilar
- Molecular Oncology Group, Department of Pharmaceuticals, Biomedical Research Division, Center for Genetic Engineering and Biotechnology, Havana 10600, Cuba; (A.C.R.); (G.V.P.); (E.C.); (M.R.); (D.A.)
| | - Dania Vázquez-Blomquist
- Pharmacogenomic Group, Department of System Biology, Biomedical Research Division, Center for Genetic Engineering and Biotechnology, Havana 10600, Cuba;
| | - Yassel Ramos
- Mass Spectrometry Laboratory, Proteomics Group, Department of Systems Biology, Biomedical Research Division, Center for Genetic Engineering and Biotechnology, Havana 10600, Cuba; (Y.R.); (A.R.-U.)
| | - Arielis Rodríguez-Ulloa
- Mass Spectrometry Laboratory, Proteomics Group, Department of Systems Biology, Biomedical Research Division, Center for Genetic Engineering and Biotechnology, Havana 10600, Cuba; (Y.R.); (A.R.-U.)
| | - Viviana Falcón
- Microscopy Laboratory, Department of System Biology, Biomedical Research Division, Center for Genetic Engineering and Biotechnology, Havana 10600, Cuba;
| | - María Pilar Rodríguez-Moltó
- Department of Agricultural Research, Animal Biotechnology Division, Center for Genetic Engineering and Biotechnology, Havana 10600, Cuba;
| | - Ke Yang
- China-Cuba Biotechnology Joint Innovation Center, Yongzhou Zhong Gu Biotechnology, Yongzhou 425000, China
| | - Yasser Perera
- Molecular Oncology Group, Department of Pharmaceuticals, Biomedical Research Division, Center for Genetic Engineering and Biotechnology, Havana 10600, Cuba; (A.C.R.); (G.V.P.); (E.C.); (M.R.); (D.A.)
- China-Cuba Biotechnology Joint Innovation Center, Yongzhou Zhong Gu Biotechnology, Yongzhou 425000, China
| | - Silvio E. Perea
- Molecular Oncology Group, Department of Pharmaceuticals, Biomedical Research Division, Center for Genetic Engineering and Biotechnology, Havana 10600, Cuba; (A.C.R.); (G.V.P.); (E.C.); (M.R.); (D.A.)
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22
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Yamazaki T, Liu L, Manley JL. Oxidative stress induces Ser 2 dephosphorylation of the RNA polymerase II CTD and premature transcription termination. Transcription 2021; 12:277-293. [PMID: 34874799 DOI: 10.1080/21541264.2021.2009421] [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] [Indexed: 01/04/2023] Open
Abstract
The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) consists of YSPTSPS heptapeptide repeats, and the phosphorylation status of the repeats controls multiple transcriptional steps and co-transcriptional events. However, how CTD phosphorylation status responds to distinct environmental stresses is not fully understood. In this study, we found that a drastic reduction in phosphorylation of a subset of Ser2 residues occurs rapidly but transiently following exposure to H2O2. ChIP analysis indicated that Ser2-P, and to a lesser extent Tyr1-P was reduced only at the gene 3' end. Significantly, the levels of polyadenylation factor CstF77, as well as Pol II, were also reduced. However, no increase in uncleaved or readthrough RNA products was observed, suggesting transcribing Pol II prematurely terminates at the gene end in response to H2O2. Further analysis found that the reduction of Ser2-P is, at least in part, regulated by CK2 but independent of FCP1 and other known Ser2 phosphatases. Finally, the H2O2 treatment also affected snRNA 3' processing although surprisingly the U2 processing was not impaired. Together, our data suggest that H2O2 exposure creates a unique CTD phosphorylation state that rapidly alters transcription to deal with acute oxidative stress, perhaps creating a novel "emergency brake" mechanism to transiently dampen gene expression.
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Affiliation(s)
- Takashi Yamazaki
- Department of Biological Sciences, Columbia University, New York, NY USA
| | - Lizhi Liu
- Department of Biological Sciences, Columbia University, New York, NY USA
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, NY USA
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23
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Braun C, Katholnig K, Kaltenecker C, Linke M, Sukhbaatar N, Hengstschläger M, Weichhart T. p38 regulates the tumor suppressor PDCD4 via the TSC-mTORC1 pathway. Cell Stress 2021; 5:176-182. [PMID: 34917890 PMCID: PMC8645265 DOI: 10.15698/cst2021.12.260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 11/21/2022] Open
Abstract
Programmed cell death protein 4 (PDCD4) exerts critical functions as tumor suppressor and in immune cells to regulate inflammatory processes. The phosphoinositide 3-kinase (PI3K) promotes degradation of PDCD4 via mammalian target of rapamycin complex 1 (mTORC1). However, additional pathways that may regulate PDCD4 expression are largely ill-defined. In this study, we have found that activation of the mitogen-activated protein kinase p38 promoted degradation of PDCD4 in macrophages and fibroblasts. Mechanistically, we identified a pathway from p38 and its substrate MAP kinase-activated protein kinase 2 (MK2) to the tuberous sclerosis complex (TSC) to regulate mTORC1-dependent degradation of PDCD4. Moreover, we provide evidence that TSC1 and TSC2 regulate PDCD4 expression via an additional mechanism independent of mTORC1. These novel data extend our knowledge of how PDCD4 expression is regulated by stress- and nutrient-sensing pathways.
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Affiliation(s)
- Clarissa Braun
- Center of Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
- Clinical Division of Endocrinology and Metabolism, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Karl Katholnig
- Center of Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Christopher Kaltenecker
- Department of Internal Medicine III, Division of Nephrology and Dialysis, Medical University of Vienna, Vienna, Austria
| | - Monika Linke
- Center of Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Nyamdelger Sukhbaatar
- Center of Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Markus Hengstschläger
- Center of Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Thomas Weichhart
- Center of Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
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24
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Sato K, Padgaonkar AA, Baker SJ, Cosenza SC, Rechkoblit O, Subbaiah DRCV, Domingo-Domenech J, Bartkowski A, Port ER, Aggarwal AK, Ramana Reddy MV, Irie HY, Reddy EP. Simultaneous CK2/TNIK/DYRK1 inhibition by 108600 suppresses triple negative breast cancer stem cells and chemotherapy-resistant disease. Nat Commun 2021; 12:4671. [PMID: 34344863 PMCID: PMC8333338 DOI: 10.1038/s41467-021-24878-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 07/08/2021] [Indexed: 02/07/2023] Open
Abstract
Triple negative breast cancer (TNBC) remains challenging because of heterogeneous responses to chemotherapy. Incomplete response is associated with a greater risk of metastatic progression. Therefore, treatments that target chemotherapy-resistant TNBC and enhance chemosensitivity would improve outcomes for these high-risk patients. Breast cancer stem cell-like cells (BCSCs) have been proposed to represent a chemotherapy-resistant subpopulation responsible for tumor initiation, progression and metastases. Targeting this population could lead to improved TNBC disease control. Here, we describe a novel multi-kinase inhibitor, 108600, that targets the TNBC BCSC population. 108600 treatment suppresses growth, colony and mammosphere forming capacity of BCSCs and induces G2M arrest and apoptosis of TNBC cells. In vivo, 108600 treatment of mice bearing triple negative tumors results in the induction of apoptosis and overcomes chemotherapy resistance. Finally, treatment with 108600 and chemotherapy suppresses growth of pre-established TNBC metastases, providing additional support for the clinical translation of this agent to clinical trials.
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Affiliation(s)
- Katsutoshi Sato
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amol A Padgaonkar
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stacey J Baker
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stephen C Cosenza
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Olga Rechkoblit
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - D R C Venkata Subbaiah
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Alison Bartkowski
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elisa R Port
- Department of Surgery, Mount Sinai Hospital, New York, NY, USA
| | - Aneel K Aggarwal
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M V Ramana Reddy
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hanna Y Irie
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - E Premkumar Reddy
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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25
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Wei H, Yang W, Hong H, Yan Z, Qin H, Benveniste EN. Protein Kinase CK2 Regulates B Cell Development and Differentiation. THE JOURNAL OF IMMUNOLOGY 2021; 207:799-808. [PMID: 34301844 DOI: 10.4049/jimmunol.2100059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/27/2021] [Indexed: 12/27/2022]
Abstract
Protein kinase CK2 (also known as Casein Kinase 2) is a serine/threonine kinase composed of two catalytic subunits (CK2α and/or CK2α') and two regulatory CK2β subunits. CK2 is overexpressed and overactive in B cell acute lymphoblastic leukemia and diffuse large B cell lymphomas, leading to inappropriate activation of the NF-κB, JAK/STAT, and PI3K/AKT/mTOR signaling pathways and tumor growth. However, whether CK2 regulates normal B cell development and differentiation is not known. We generated mice lacking CK2α specifically in B cells (using CD19-driven Cre recombinase). These mice exhibited cell-intrinsic expansion of marginal zone B cells at the expense of transitional B cells, without changes in follicular B cells. Transitional B cells required CK2α to maintain adequate BCR signaling. In the absence of CK2α, reduced BCR signaling and elevated Notch2 signaling activation increased marginal zone B cell differentiation. Our results identify a previously unrecognized function for CK2α in B cell development and differentiation.
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Affiliation(s)
- Hairong Wei
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294; and
| | - Wei Yang
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294; and
| | - Huixian Hong
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294; and
| | - Zhaoqi Yan
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294; and.,Gladstone Institute of Neurological Disease, San Francisco, CA 94158
| | - Hongwei Qin
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294; and
| | - Etty N Benveniste
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294; and
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26
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Targeting of Protein Kinase CK2 in Acute Myeloid Leukemia Cells Using the Clinical-Grade Synthetic-Peptide CIGB-300. Biomedicines 2021; 9:biomedicines9070766. [PMID: 34356831 PMCID: PMC8301452 DOI: 10.3390/biomedicines9070766] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/24/2021] [Accepted: 06/26/2021] [Indexed: 12/15/2022] Open
Abstract
Protein kinase CK2 has emerged as an attractive therapeutic target in acute myeloid leukemia (AML), an advent that becomes particularly relevant since the treatment of this hematological neoplasia remains challenging. Here we explored for the first time the effect of the clinical-grade peptide-based CK2 inhibitor CIGB-300 on AML cells proliferation and viability. CIGB-300 internalization and subcellular distribution were also studied, and the role of B23/nucleophosmin 1 (NPM1), a major target for the peptide in solid tumors, was addressed by knock-down in model cell lines. Finally, pull-down experiments and phosphoproteomic analysis were performed to study CIGB-interacting proteins and identify the array of CK2 substrates differentially modulated after treatment with the peptide. Importantly, CIGB-300 elicited a potent anti-proliferative and proapoptotic effect in AML cells, with more than 80% of peptide transduced cells within three minutes. Unlike solid tumor cells, NPM1 did not appear to be a major target for CIGB-300 in AML cells. However, in vivo pull-down experiments and phosphoproteomic analysis evidenced that CIGB-300 targeted the CK2α catalytic subunit, different ribosomal proteins, and inhibited the phosphorylation of a common CK2 substrates array among both AML backgrounds. Remarkably, our results not only provide cellular and molecular insights unveiling the complexity of the CIGB-300 anti-leukemic effect in AML cells but also reinforce the rationale behind the pharmacologic blockade of protein kinase CK2 for AML-targeted therapy.
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27
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CX-4945 and siRNA-Mediated Knockdown of CK2 Improves Cisplatin Response in HPV(+) and HPV(-) HNSCC Cell Lines. Biomedicines 2021; 9:biomedicines9050571. [PMID: 34070147 PMCID: PMC8158385 DOI: 10.3390/biomedicines9050571] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 12/24/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) can be categorized into human papillomavirus (HPV) positive or negative disease. Elevated protein kinase CK2 level and activity have been historically observed in HNSCC cells. Previous studies on CK2 in HNSCC did not generally include consideration of HPV(+) and HPV(−) status. Here, we investigated the response of HPV(+) and HPV(−) HNSCC cells to CK2 targeting using CX-4945 or siRNA downregulation combined with cisplatin treatment. HNSCC cell lines were examined for CK2 expression levels and activity and response to CX-4945, with and without cisplatin. CK2 levels and NFκB p65-related activity were high in HPV(+) HNSCC cells relative to HPV(−) HNSCC cells. Treatment with CX-4945 decreased viability and cisplatin IC50 in all cell lines. Targeting of CK2 increased tumor suppressor protein levels for p21 and PDCD4 in most instances. Further study is needed to understand the role of CK2 in HPV(+) and HPV(−) HNSCC and to determine how incorporation of the CK2-targeted inhibitor CX-4945 could improve cisplatin response in HNSCC.
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Baier A, Kokel A, Horton W, Gizińska E, Pandey G, Szyszka R, Török B, Török M. Organofluorine Hydrazone Derivatives as Multifunctional Anti-Alzheimer's Agents with CK2 Inhibitory and Antioxidant Features. ChemMedChem 2021; 16:1927-1932. [PMID: 33713036 DOI: 10.1002/cmdc.202100047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Indexed: 11/10/2022]
Abstract
A set of novel hydrazone derivatives were synthesized and analyzed for their biological activities. The compounds were tested for their inhibitory effect on the phosphorylating activity of the protein kinase CK2, and their antioxidant activity was also determined in three commonly used assays. The hydrazones were evaluated for their radical scavenging against the DPPH, ABTS and peroxyl radicals. Several compounds have been identified as good antioxidants as well as potent protein kinase CK2 inhibitors. Most hydrazones containing a 4-N(CH3 )2 residue or perfluorinated phenyl rings showed high activity in the radical-scavenging assays and possess nanomolar IC50 values in the kinase assays.
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Affiliation(s)
- Andrea Baier
- Department of Animal Physiology and Toxicology, The John Paul II Catholic University of Lublin, ul. Konstantynów 1i, 20-708, Lublin, Poland
| | - Anne Kokel
- Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Blvd, Boston, MA, 02125, USA
| | - William Horton
- Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Blvd, Boston, MA, 02125, USA
| | - Ewa Gizińska
- Department of Molecular Biology, The John Paul II Catholic University of Lublin, ul. Konstantynów 1i, 20-708, Lublin, Poland
| | - Garima Pandey
- Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Blvd, Boston, MA, 02125, USA
| | - Ryszard Szyszka
- Department of Molecular Biology, The John Paul II Catholic University of Lublin, ul. Konstantynów 1i, 20-708, Lublin, Poland
| | - Béla Török
- Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Blvd, Boston, MA, 02125, USA
| | - Marianna Török
- Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Blvd, Boston, MA, 02125, USA
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Hitz E, Grüninger O, Passecker A, Wyss M, Scheurer C, Wittlin S, Beck HP, Brancucci NMB, Voss TS. The catalytic subunit of Plasmodium falciparum casein kinase 2 is essential for gametocytogenesis. Commun Biol 2021; 4:336. [PMID: 33712726 PMCID: PMC7954856 DOI: 10.1038/s42003-021-01873-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 02/17/2021] [Indexed: 01/31/2023] Open
Abstract
Casein kinase 2 (CK2) is a pleiotropic kinase phosphorylating substrates in different cellular compartments in eukaryotes. In the malaria parasite Plasmodium falciparum, PfCK2 is vital for asexual proliferation of blood-stage parasites. Here, we applied CRISPR/Cas9-based gene editing to investigate the function of the PfCK2α catalytic subunit in gametocytes, the sexual forms of the parasite that are essential for malaria transmission. We show that PfCK2α localizes to the nucleus and cytoplasm in asexual and sexual parasites alike. Conditional knockdown of PfCK2α expression prevented the transition of stage IV into transmission-competent stage V gametocytes, whereas the conditional knockout of pfck2a completely blocked gametocyte maturation already at an earlier stage of sexual differentiation. In summary, our results demonstrate that PfCK2α is not only essential for asexual but also sexual development of P. falciparum blood-stage parasites and encourage studies exploring PfCK2α as a potential target for dual-active antimalarial drugs.
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Affiliation(s)
- Eva Hitz
- grid.416786.a0000 0004 0587 0574Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland ,grid.6612.30000 0004 1937 0642University of Basel, 4001 Basel, Switzerland
| | - Olivia Grüninger
- grid.416786.a0000 0004 0587 0574Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland ,grid.6612.30000 0004 1937 0642University of Basel, 4001 Basel, Switzerland
| | - Armin Passecker
- grid.416786.a0000 0004 0587 0574Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland ,grid.6612.30000 0004 1937 0642University of Basel, 4001 Basel, Switzerland
| | - Matthias Wyss
- grid.416786.a0000 0004 0587 0574Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland ,grid.6612.30000 0004 1937 0642University of Basel, 4001 Basel, Switzerland
| | - Christian Scheurer
- grid.416786.a0000 0004 0587 0574Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland ,grid.6612.30000 0004 1937 0642University of Basel, 4001 Basel, Switzerland
| | - Sergio Wittlin
- grid.416786.a0000 0004 0587 0574Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland ,grid.6612.30000 0004 1937 0642University of Basel, 4001 Basel, Switzerland
| | - Hans-Peter Beck
- grid.416786.a0000 0004 0587 0574Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland ,grid.6612.30000 0004 1937 0642University of Basel, 4001 Basel, Switzerland
| | - Nicolas M. B. Brancucci
- grid.416786.a0000 0004 0587 0574Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland ,grid.6612.30000 0004 1937 0642University of Basel, 4001 Basel, Switzerland
| | - Till S. Voss
- grid.416786.a0000 0004 0587 0574Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland ,grid.6612.30000 0004 1937 0642University of Basel, 4001 Basel, Switzerland
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Rosales M, Rodríguez-Ulloa A, Besada V, Ramón AC, Pérez GV, Ramos Y, Guirola O, González LJ, Zettl K, Wiśniewski JR, Perera Y, Perea SE. Phosphoproteomic Landscape of AML Cells Treated with the ATP-Competitive CK2 Inhibitor CX-4945. Cells 2021; 10:cells10020338. [PMID: 33562780 PMCID: PMC7915770 DOI: 10.3390/cells10020338] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/30/2021] [Accepted: 02/02/2021] [Indexed: 12/13/2022] Open
Abstract
Casein kinase 2 (CK2) regulates a plethora of proteins with pivotal roles in solid and hematological neoplasia. Particularly, in acute myeloid leukemia (AML) CK2 has been pointed as an attractive therapeutic target and prognostic marker. Here, we explored the impact of CK2 inhibition over the phosphoproteome of two cell lines representing major AML subtypes. Quantitative phosphoproteomic analysis was conducted to evaluate changes in phosphorylation levels after incubation with the ATP-competitive CK2 inhibitor CX-4945. Functional enrichment, network analysis, and database mining were performed to identify biological processes, signaling pathways, and CK2 substrates that are responsive to CX-4945. A total of 273 and 1310 phosphopeptides were found differentially modulated in HL-60 and OCI-AML3 cells, respectively. Despite regulated phosphopeptides belong to proteins involved in multiple biological processes and signaling pathways, most of these perturbations can be explain by direct CK2 inhibition rather than off-target effects. Furthermore, CK2 substrates regulated by CX-4945 are mainly related to mRNA processing, translation, DNA repair, and cell cycle. Overall, we evidenced that CK2 inhibitor CX-4945 impinge on mediators of signaling pathways and biological processes essential for primary AML cells survival and chemosensitivity, reinforcing the rationale behind the pharmacologic blockade of protein kinase CK2 for AML targeted therapy.
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Affiliation(s)
- Mauro Rosales
- Department of Animal and Human Biology, Faculty of Biology, University of Havana (UH), Havana 10400, Cuba;
- Molecular Oncology Group, Department of Pharmaceuticals, Biomedical Research Division, Center for Genetic Engineering and Biotechnology (CIGB), Havana 10600, Cuba; (A.C.R.); (G.V.P.)
| | - Arielis Rodríguez-Ulloa
- Mass Spectrometry Laboratory, Proteomics Group, Department of Systems Biology, Biomedical Research Division, CIGB, Havana 10600, Cuba; (A.R.-U.); (V.B.); (Y.R.); (L.J.G.)
| | - Vladimir Besada
- Mass Spectrometry Laboratory, Proteomics Group, Department of Systems Biology, Biomedical Research Division, CIGB, Havana 10600, Cuba; (A.R.-U.); (V.B.); (Y.R.); (L.J.G.)
| | - Ailyn C. Ramón
- Molecular Oncology Group, Department of Pharmaceuticals, Biomedical Research Division, Center for Genetic Engineering and Biotechnology (CIGB), Havana 10600, Cuba; (A.C.R.); (G.V.P.)
| | - George V. Pérez
- Molecular Oncology Group, Department of Pharmaceuticals, Biomedical Research Division, Center for Genetic Engineering and Biotechnology (CIGB), Havana 10600, Cuba; (A.C.R.); (G.V.P.)
| | - Yassel Ramos
- Mass Spectrometry Laboratory, Proteomics Group, Department of Systems Biology, Biomedical Research Division, CIGB, Havana 10600, Cuba; (A.R.-U.); (V.B.); (Y.R.); (L.J.G.)
| | - Osmany Guirola
- Bioinformatics Group, Department of Systems Biology, Biomedical Research Division, CIGB, Havana 10600, Cuba;
| | - Luis J. González
- Mass Spectrometry Laboratory, Proteomics Group, Department of Systems Biology, Biomedical Research Division, CIGB, Havana 10600, Cuba; (A.R.-U.); (V.B.); (Y.R.); (L.J.G.)
| | - Katharina Zettl
- Biochemical Proteomics Group, Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, 82152 Munich, Germany; (K.Z.); (J.R.W.)
| | - Jacek R. Wiśniewski
- Biochemical Proteomics Group, Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, 82152 Munich, Germany; (K.Z.); (J.R.W.)
| | - Yasser Perera
- Molecular Oncology Group, Department of Pharmaceuticals, Biomedical Research Division, Center for Genetic Engineering and Biotechnology (CIGB), Havana 10600, Cuba; (A.C.R.); (G.V.P.)
- China-Cuba Biotechnology Joint Innovation Center (CCBJIC), Yongzhou Zhong Gu Biotechnology Co., Ltd, Lengshuitan District, Yongzhou 425000, China
- Correspondence: (Y.P.); (S.E.P.)
| | - Silvio E. Perea
- Molecular Oncology Group, Department of Pharmaceuticals, Biomedical Research Division, Center for Genetic Engineering and Biotechnology (CIGB), Havana 10600, Cuba; (A.C.R.); (G.V.P.)
- Correspondence: (Y.P.); (S.E.P.)
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Bhardwaj P, Kulasiri D, Samarasinghe S. Modeling protein-protein interactions in axon initial segment to understand their potential impact on action potential initiation. Neural Regen Res 2021; 16:700-706. [PMID: 33063731 PMCID: PMC8067952 DOI: 10.4103/1673-5374.295332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The axon initial segment (AIS) region is crucial for action potential initiation due to the presence of high-density AIS protein voltage-gated sodium channels (Nav). Nav channels comprise several serine residues responsible for the recruitment of Nav channels into the structure of AIS through interactions with ankyrin-G (AnkG). In this study, a series of computational experiments are performed to understand the role of AIS proteins casein kinase 2 and AnkG on Nav channel recruitment into the AIS. The computational simulation results using Virtual cell software indicate that Nav channels with all serine sites available for phosphorylation bind to AnkG with strong affinity. At the low initial concentration of AnkG and casein kinase 2, the concentration of Nav channels reduces significantly, suggesting the importance of casein kinase 2 and AnkG in the recruitment of Nav channels.
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Affiliation(s)
- Piyush Bhardwaj
- Centre of Advanced Computational Solutions (C-fACS); Department of Molecular Biosciences, Lincoln University, Christchurch, New Zealand
| | - Don Kulasiri
- Centre of Advanced Computational Solutions (C-fACS); Department of Molecular Biosciences, Lincoln University, Christchurch, New Zealand
| | - Sandhya Samarasinghe
- Centre of Advanced Computational Solutions (C-fACS), Lincoln University, Christchurch, New Zealand
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32
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Ou J, Liu H, Nirala NK, Stukalov A, Acharya U, Green MR, Zhu LJ. dagLogo: An R/Bioconductor package for identifying and visualizing differential amino acid group usage in proteomics data. PLoS One 2020; 15:e0242030. [PMID: 33156866 PMCID: PMC7647101 DOI: 10.1371/journal.pone.0242030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 10/23/2020] [Indexed: 11/18/2022] Open
Abstract
Sequence logos have been widely used as graphical representations of conserved nucleic acid and protein motifs. Due to the complexity of the amino acid (AA) alphabet, rich post-translational modification, and diverse subcellular localization of proteins, few versatile tools are available for effective identification and visualization of protein motifs. In addition, various reduced AA alphabets based on physicochemical, structural, or functional properties have been valuable in the study of protein alignment, folding, structure prediction, and evolution. However, there is lack of tools for applying reduced AA alphabets to the identification and visualization of statistically significant motifs. To fill this gap, we developed an R/Bioconductor package dagLogo, which has several advantages over existing tools. First, dagLogo allows various formats for input sets and provides comprehensive options to build optimal background models. It implements different reduced AA alphabets to group AAs of similar properties. Furthermore, dagLogo provides statistical and visual solutions for differential AA (or AA group) usage analysis of both large and small data sets. Case studies showed that dagLogo can better identify and visualize conserved protein sequence patterns from different types of inputs and can potentially reveal the biological patterns that could be missed by other logo generators.
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Affiliation(s)
- Jianhong Ou
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Regeneration NEXT, Duke University School of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Haibo Liu
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Niraj K. Nirala
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Alexey Stukalov
- Institute of Virology, Technical University of Munich, Munich, Germany
| | - Usha Acharya
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Michael R. Green
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Lihua Julie Zhu
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
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33
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Protein kinase 2 (CK2) controls CD4 + T cell effector function in the pathogenesis of colitis. Mucosal Immunol 2020; 13:788-798. [PMID: 31988467 PMCID: PMC7382987 DOI: 10.1038/s41385-020-0258-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 01/03/2020] [Accepted: 01/08/2020] [Indexed: 02/04/2023]
Abstract
Crohn's disease (CD), one of the major forms of inflammatory bowel disease (IBD), is characterized by chronic inflammation of the gastrointestinal tract and associated with aberrant CD4+ T-helper type 1 (Th1) and Th17 responses. Protein kinase 2 (CK2) is a conserved serine-threonine kinase involved in signal transduction pathways, which regulate immune responses. CK2 promotes Th17 cell differentiation and suppresses the generation of Foxp3+ regulatory T cells. The function of CK2 in CD4+ T cells during the pathogenesis of CD is unknown. We utilized the T cell-induced colitis model, transferring CD45RBhi-naive CD4+ T cells from CK2αfl/fl controls and CK2αfl/fldLck-Cre mice into Rag1-/- mice. CD4+ T cells from CK2αfl/fldLck-Cre mice failed to induce wasting disease and significant intestinal inflammation, which was associated with decreased interleukin-17A-positive (IL-17A+), interferon-γ-positive (IFN-γ+), and double-positive IL-17A+IFN-γ+ CD4+ T cells in the spleen and colon. We determined that CK2α regulates CD4+ T cell proliferation through a cell-intrinsic manner. CK2α is also important in controlling CD4+ T cell responses by regulating NFAT2, which is vital for T cell activation and proliferation. Our findings indicate that CK2α contributes to the pathogenesis of colitis by promoting CD4+ T cell proliferation and Th1 and Th17 responses, and that targeting CK2 may be a novel therapeutic treatment for patients with CD.
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Krämer A, Kurz CG, Berger BT, Celik IE, Tjaden A, Greco FA, Knapp S, Hanke T. Optimization of pyrazolo[1,5-a]pyrimidines lead to the identification of a highly selective casein kinase 2 inhibitor. Eur J Med Chem 2020; 208:112770. [PMID: 32883634 DOI: 10.1016/j.ejmech.2020.112770] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/09/2020] [Accepted: 08/15/2020] [Indexed: 12/13/2022]
Abstract
Casein kinase 2 (CK2) is a constitutively expressed serine/threonine kinase that has a large diversity of cellular substrates. Thus, CK2 has been associated with a plethora of regulatory functions and dysregulation of CK2 has been linked to disease development in particular to cancer. The broad implications in disease pathology makes CK2 an attractive target. To date, the most advanced CK2 inhibitor is silmitasertib, which has been investigated in clinical trials for treatment of various cancers, albeit several off-targets for silmitasertib have been described. To ascertain the role of CK2 inhibition in cancer, other disease and normal physiology the development of a selective CK2 inhibitor would be highly desirable. In this study we explored the pyrazolo [1,5-a]pyrimidine hinge-binding moiety for the development of selective CK2 inhibitors. Optimization of this scaffold, which included macrocyclization, led to IC20 (31) a compound that displayed high in vitro potency for CK2 (KD = 12 nM) and exclusive selectivity for CK2. X-ray analysis revealed a canonical type-I binding mode for IC20 (31). However, the polar carboxylic acid moiety that is shared by many CK2 inhibitors including silmitasertib was required for potency but limits the cellular activity of IC20 (31) and the cellular IC50 dropped to the low micromolar range. In summary, IC20 (31) represents a highly selective and potent inhibitor of CK2, which can be used as a tool compound to study CK2 biology and potential new applications for the treatment of diseases.
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Affiliation(s)
- Andreas Krämer
- Institute of Pharmaceutical Chemistry, Max-von-Laue-Straße 9, Goethe University Frankfurt, 60438, Frankfurt, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Straße 15, 60438, Frankfurt, Germany; Frankfurt Cancer Institute (FCI), Paul-Ehrlich-Straße 42-44, 60596, Frankfurt Am Main, Germany
| | - Christian Georg Kurz
- Institute of Pharmaceutical Chemistry, Max-von-Laue-Straße 9, Goethe University Frankfurt, 60438, Frankfurt, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Straße 15, 60438, Frankfurt, Germany
| | - Benedict-Tilman Berger
- Institute of Pharmaceutical Chemistry, Max-von-Laue-Straße 9, Goethe University Frankfurt, 60438, Frankfurt, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Straße 15, 60438, Frankfurt, Germany
| | - Ibrahim Ethem Celik
- Institute of Pharmaceutical Chemistry, Max-von-Laue-Straße 9, Goethe University Frankfurt, 60438, Frankfurt, Germany
| | - Amelie Tjaden
- Institute of Pharmaceutical Chemistry, Max-von-Laue-Straße 9, Goethe University Frankfurt, 60438, Frankfurt, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Straße 15, 60438, Frankfurt, Germany
| | - Francesco Aleksy Greco
- Institute of Pharmaceutical Chemistry, Max-von-Laue-Straße 9, Goethe University Frankfurt, 60438, Frankfurt, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Straße 15, 60438, Frankfurt, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Max-von-Laue-Straße 9, Goethe University Frankfurt, 60438, Frankfurt, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Straße 15, 60438, Frankfurt, Germany; German Translational Cancer Network (DKTK) Site Frankfurt/Mainz, Germany; Frankfurt Cancer Institute (FCI), Paul-Ehrlich-Straße 42-44, 60596, Frankfurt Am Main, Germany.
| | - Thomas Hanke
- Institute of Pharmaceutical Chemistry, Max-von-Laue-Straße 9, Goethe University Frankfurt, 60438, Frankfurt, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Straße 15, 60438, Frankfurt, Germany.
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Ibrahim HA, Refaat HM. Versatile mechanisms of 2-substituted benzimidazoles in targeted cancer therapy. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2020. [DOI: 10.1186/s43094-020-00048-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Abstract
Background
The aim of this review is to provide an overview on diverse anticancer activities of 2-substituted benzimidazole derivatives.
Main body
This review provides a correlation between the various mechanisms of action of benzimidazoles as anticancer and the substitution pattern around the nucleus.
Conclusion
The linker group and substitution at N-1, C-2, C-5, and C-6 positions have been found to be the most contributory factors for anticancer activity. This will help in the further design to afford more selective, potent, and multi-target anticancer of 2-substituted benzimidazole-based compounds.
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Sampadi B, Pines A, Munk S, Mišovic B, de Groot AJ, van de Water B, Olsen JV, Mullenders LHF, Vrieling H. Quantitative phosphoproteomics to unravel the cellular response to chemical stressors with different modes of action. Arch Toxicol 2020; 94:1655-1671. [PMID: 32189037 PMCID: PMC7261734 DOI: 10.1007/s00204-020-02712-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 03/09/2020] [Indexed: 12/02/2022]
Abstract
Damage to cellular macromolecules and organelles by chemical exposure evokes activation of various stress response pathways. To what extent different chemical stressors activate common and stressor-specific pathways is largely unknown. Here, we used quantitative phosphoproteomics to compare the signaling events induced by four stressors with different modes of action: the DNA damaging agent: cisplatin (CDDP), the topoisomerase II inhibitor: etoposide (ETO), the pro-oxidant: diethyl maleate (DEM) and the immunosuppressant: cyclosporine A (CsA) administered at an equitoxic dose to mouse embryonic stem cells. We observed major differences between the stressors in the number and identity of responsive phosphosites and the amplitude of phosphorylation. Kinase motif and pathway analyses indicated that the DNA damage response (DDR) activation by CDDP occurs predominantly through the replication-stress-related Atr kinase, whereas ETO triggers the DDR through Atr as well as the DNA double-strand-break-associated Atm kinase. CsA shares with ETO activation of CK2 kinase. Congruent with their known modes of action, CsA-mediated signaling is related to down-regulation of pathways that control hematopoietic differentiation and immunity, whereas oxidative stress is the most prominent initiator of DEM-modulated stress signaling. This study shows that even at equitoxic doses, different stressors induce distinctive and complex phosphorylation signaling cascades.
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Affiliation(s)
- Bharath Sampadi
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Alex Pines
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Stephanie Munk
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark
| | - Branislav Mišovic
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Anton J de Groot
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark
| | - Leon H F Mullenders
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
| | - Harry Vrieling
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands.
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Demulder M, De Veylder L, Loris R. Crystal structure of Arabidopsis thaliana casein kinase 2 α1. Acta Crystallogr F Struct Biol Commun 2020; 76:182-191. [PMID: 32254052 PMCID: PMC7137383 DOI: 10.1107/s2053230x20004537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/01/2020] [Indexed: 11/11/2022] Open
Abstract
Casein kinase 2 (CK2) is a ubiquitous pleiotropic enzyme that is highly conserved across eukaryotic kingdoms. CK2 is singular amongst kinases as it is highly rigid and constitutively active. Arabidopsis thaliana is widely used as a model system in molecular plant research; the biological functions of A. thaliana CK2 are well studied in vivo and many of its substrates have been identified. Here, crystal structures of the α subunit of A. thaliana CK2 in three crystal forms and of its complex with the nonhydrolyzable ATP analog AMppNHp are presented. While the C-lobe of the enzyme is highly rigid, structural plasticity is observed for the N-lobe. Small but significant displacements within the active cleft are necessary in order to avoid steric clashes with the AMppNHp molecule. Binding of AMppNHp is influenced by a rigid-body motion of the N-lobe that was not previously recognized in maize CK2.
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Affiliation(s)
- Manon Demulder
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
- Center for Structural Biology, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052 Ghent, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark 71, B-9052 Ghent, Belgium
| | - Remy Loris
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
- Center for Structural Biology, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
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Zhang C, Li H, Yuan C, Liu S, Li M, Zhu J, Lin X, Lu Y, Guo X. CKB1 regulates expression of ribosomal protein L10 family gene and plays a role in UV-B response. PLANT BIOLOGY (STUTTGART, GERMANY) 2020; 22 Suppl 1:143-152. [PMID: 30597713 DOI: 10.1111/plb.12954] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 12/22/2018] [Indexed: 06/09/2023]
Abstract
Plastid casein kinase 2 (CK2), which is a major Ser/Thr-specific enzyme in higher organisms, plays an essential role in plant development and diverse abiotic stresses. CKB1 is a regulatory subunit beta of CK2. To expand our understand of functions of the CKB1 gene in Arabidopsis thaliana, protein changes among wild-type (WT) and CKB1 gain- and loss-of-function mutants were compared. Proteins extracted from the CKB1 knockout mutant and overexpressing mutant were compared with Col-0 plants using 2D-PAGE. Proteins regulated by CKB1 were identified with matrix-assisted laser desorption ionisation time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF), and its transcript was verified by qRT-PCR. Bioinformatics analysis, including gene ontology and protein-protein interaction analysis, were employed. The results of mass spectra and bioinformatics analysis suggest that CKB1 may have functions in regulation of the ribosomal protein L10 (RPL10) family and is involved in ultraviolet-B (UV-B) response. Furthermore, qRT-PCR verification showed CKB1 expression was up-regulated by UV-B stress. The expression levels of five genes in the RPL10 family were reduced in the ckb1 T-DNA insertion mutants, whereas they increased in the CKB1 overexpressing mutants under both normal conditions and UV-B treatment. In conclusion, CKB1 has important functions in UV-B radiation stress. Our study implies that CKB1 positively regulates UV-B radiation stress signalling, possibly through modulating expression of the RPL10 family.
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Affiliation(s)
- C Zhang
- College of Life Sciences, Hunan University, Changsha, China
| | - H Li
- College of Life Sciences, Hunan University, Changsha, China
| | - C Yuan
- College of Life Sciences, Hunan University, Changsha, China
| | - S Liu
- College of Life Sciences, Hunan University, Changsha, China
| | - M Li
- College of Life Sciences, Hunan University, Changsha, China
| | - J Zhu
- College of Life Sciences, Hunan University, Changsha, China
| | - X Lin
- College of Life Sciences, Hunan University, Changsha, China
| | - Y Lu
- College of Life Sciences, Hunan University, Changsha, China
| | - X Guo
- College of Life Sciences, Hunan University, Changsha, China
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Mapping and functional analysis of heterochromatin protein 1 phosphorylation in the malaria parasite Plasmodium falciparum. Sci Rep 2019; 9:16720. [PMID: 31723180 PMCID: PMC6853920 DOI: 10.1038/s41598-019-53325-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 10/30/2019] [Indexed: 01/01/2023] Open
Abstract
Previous studies in model eukaryotes have demonstrated that phosphorylation of heterochromatin protein 1 (HP1) is important for dynamically regulating its various functions. However, in the malaria parasite Plasmodium falciparum both the function of HP1 phosphorylation and the identity of the protein kinases targeting HP1 are still elusive. In order to functionally analyze phosphorylation of P. falciparum HP1 (PfHP1), we first mapped PfHP1 phosphorylation sites by liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis of native PfHP1, which identified motifs from which potential kinases could be predicted; in particular, several phosphorylated residues were embedded in motifs rich in acidic residues, reminiscent of targets for P. falciparum casein kinase 2 (PfCK2). Secondly, we tested recombinant PfCK2 and a number of additional protein kinases for their ability to phosphorylate PfHP1 in in vitro kinase assays. These experiments validated our prediction that PfHP1 acts as a substrate for PfCK2. Furthermore, LC-MS/MS analysis showed that PfCK2 phosphorylates three clustered serine residues in an acidic motif within the central hinge region of PfHP1. To study the role of PfHP1 phosphorylation in live parasites we used CRISPR/Cas9-mediated genome editing to generate a number of conditional PfHP1 phosphomutants based on the DiCre/LoxP system. Our studies revealed that neither PfCK2-dependent phosphorylation of PfHP1, nor phosphorylation of the hinge domain in general, affect PfHP1's ability to localize to heterochromatin, and that PfHP1 phosphorylation in this region is dispensable for the proliferation of P. falciparum blood stage parasites.
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Rahm M, Merl-Pham J, Adamski J, Hauck SM. Time-resolved phosphoproteomic analysis elucidates hepatic 11,12-Epoxyeicosatrienoic acid signaling pathways. Prostaglandins Other Lipid Mediat 2019; 146:106387. [PMID: 31669255 DOI: 10.1016/j.prostaglandins.2019.106387] [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: 05/20/2019] [Revised: 09/24/2019] [Accepted: 10/16/2019] [Indexed: 01/20/2023]
Abstract
Epoxyeicosatrienoic acids (EETs) are potent lipid mediators with well-established effects in vascular tissues. Recent studies indicated an emerging role of these eicosanoids in metabolic diseases and the EET signaling pathway was shown to be involved in hepatic insulin sensitivity. However, compared to vascular tissues, there is only limited knowledge about the underlying signaling pathways in the liver. Therefore, we employed an LC-MS/MS-based time-resolved phosphoproteomics approach to characterize 11,12-EET-mediated signaling events in the liver cell line Hepa 1-6. 11,12-EET treatment resulted in the time-dependent regulation of phosphopeptides involved in processes as yet unknown to be affected by EETs, including RNA processing, splicing and translation regulation. Pathway analysis combined with western blot-based validation revealed enhanced AKT/mTOR/p70S6K signaling as demonstrated by increased acute phosphorylation of AKT (Ser473) and p70S6K (Thr389). In addition, 11,12-EET treatment led to differential regulation of phosphopeptides including important mediators of the DNA damage response and we observed a prolonged induction of the etoposide-induced DNA damage marker γH2AX in response to 11,12-EET. In summary, our findings extend current knowledge of 11,12-EET signaling events and emphasize the importance of the AKT/mTOR/p70S6K pathway in hepatic 11,12-EET signaling. Based on the results presented in this study, we furthermore propose a novel role of EET signaling in the regulation of the DNA damage response.
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Affiliation(s)
- Marco Rahm
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Juliane Merl-Pham
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Jerzy Adamski
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany.
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Sukocheva O, Menschikowski M, Hagelgans A, Yarla NS, Siegert G, Reddanna P, Bishayee A. Current insights into functions of phospholipase A2 receptor in normal and cancer cells: More questions than answers. Semin Cancer Biol 2019; 56:116-127. [PMID: 29104026 DOI: 10.1016/j.semcancer.2017.11.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/18/2017] [Accepted: 11/01/2017] [Indexed: 02/08/2023]
Abstract
Lipid signaling network was proposed as a potential target for cancer prevention and treatment. Several recent studies revealed that phospholipid metabolising enzyme, phospholipase A2 (PLA2), is a critical regulator of cancer accelerating pathologies and apoptosis in several types of cancers. In addition to functioning as an enzyme, PLA2 can activate a phospholipase A2 receptor (PLA2R1) in plasma membrane. While the list of PLA2 targets extends to glucose homeostasis, intracellular energy balance, adipocyte development, and hepatic lipogenesis, the PLA2R1 downstream effectors are few and scarcely investigated. Among the most addressed PLA2R1 effects are regulation of pro-inflammatory signaling, autoimmunity, apoptosis, and senescence. Localized in glomeruli podocytes, the receptor can be identified by circulating anti-PLA2R1 autoantibodies leading to development of membranous nephropathy, a strong autoimmune inflammatory cascade. PLA2R1 was shown to induce activation of Janus-kinase 2 (JAK2) and estrogen-related receptor α (ERRα)-controlled mitochondrial proteins, as well as increasing the accumulation of reactive oxygen species, thus leading to apoptosis and senescence. These findings indicate the potential role of PLA2R1 as tumor suppressor. Epigenetic investigations addressed the role of DNA methylation, histone modifications, and specific microRNAs in the regulation of PLA2R1 expression. However, involvement of PLA2R1 in suppression of malignant growth and metastasis remains controversial. In this review, we summarize the recent findings that highlight the role of PLA2R1 in the regulation of carcinogenesis-related intracellular signaling.
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Affiliation(s)
- Olga Sukocheva
- School of Health Sciences, Flinders University of South Australia, Bedford Park, South Australia 5042, Australia.
| | - Mario Menschikowski
- Institute of Clinical Chemistry and Laboratory Medicine, Carl Gustav Carus University Hospital, Technical University of Dresden, Fetscherstr. 74, D-01307 Dresden, Germany
| | - Albert Hagelgans
- Institute of Clinical Chemistry and Laboratory Medicine, Carl Gustav Carus University Hospital, Technical University of Dresden, Fetscherstr. 74, D-01307 Dresden, Germany
| | - Nagendra Sastry Yarla
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, Telangana, India
| | - Gabriele Siegert
- Institute of Clinical Chemistry and Laboratory Medicine, Carl Gustav Carus University Hospital, Technical University of Dresden, Fetscherstr. 74, D-01307 Dresden, Germany
| | - Pallu Reddanna
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, Telangana, India
| | - Anupam Bishayee
- Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA.
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Michel J, Nolin F, Wortham L, Lalun N, Tchelidze P, Banchet V, Terryn C, Ploton D. Various Nucleolar Stress Inducers Result in Highly Distinct Changes in Water, Dry Mass and Elemental Content in Cancerous Cell Compartments: Investigation Using a Nano-Analytical Approach. Nanotheranostics 2019; 3:179-195. [PMID: 31183313 PMCID: PMC6536780 DOI: 10.7150/ntno.31878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/20/2019] [Indexed: 01/10/2023] Open
Abstract
Rationale: Numerous chemotherapeutic drugs that affect ribosome biogenesis in the nucleolus induce nucleolar stress. Improving our understanding of the effects of these drugs will require uncovering and comparing their impact on several biophysical parameters of the major cell compartments. Here, we quantified the water content and dry mass of cancerous cells treated with CX-5461, DRB or DAM to calculate macromolecular crowding and the volume occupied by free water, as well as elemental content. Methods: HeLa-H2B-GFP cells were treated with CX-5461, DRB or DAM. Water content and dry mass were measured in numerous regions of interest of ultrathin cryo-sections by quantitative scanning transmission electron microscope dark-field imaging and the elements quantified by energy dispersive X-ray spectrometry. The data were used to calculate macromolecular crowding and the volume occupied by free water in all cell compartments of control and treated cells. Hydrophobic and unfolded proteins were revealed by 8-Anilinonaphtalene-1-sulfonic acid (ANS) staining and imaging by two-photon microscopy. Immunolabeling of UBF, pNBS1 and pNF-κB was carried out and the images acquired with a confocal microscope for 3D imaging to address whether the localization of these proteins changes in treated cells. Results: Treatment with CX-5461, DRB or DAM induced completely different changes in macromolecular crowding and elemental content. Macromolecular crowding and elemental content were much higher in CX-5461-treated, moderately higher in DRB-treated, and much lower in DAM-treated cells than control cells. None of the drugs alone induced nucleolar ANS staining but it was induced by heat-shock of control cells and cells previously treated with DAM. UBF and pNBS1 were systematically co-localized in the nucleolus of CX-5461- and DAM-treated cells. pNF-κB only localized to the nucleolar caps of pre-apoptotic DAM-treated cells. Conclusion: We directly quantified water and ion content in cell compartments using cryo-correlative electron microscopy. We show that different chemotherapeutic nucleolar stress inducers result in distinctive, thus far-unrecognized changes in macromolecular crowding and elemental content which are known to modify cell metabolism. Moreover we were able to correlate these changes to the sensitivity of treated cells to heat-shock and the behavior of nucleolar pNBS1 and pNF-κB.
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Affiliation(s)
- Jean Michel
- UMR-S 1250 INSERM, Université de Reims Champagne Ardenne
| | | | - Laurence Wortham
- Platform of Cell and Tissue Imaging (PICT), Université de Reims Champagne Ardenne
| | - Nathalie Lalun
- UMR-S 1250 INSERM, Université de Reims Champagne Ardenne
| | - Pavel Tchelidze
- Faculty of Exact and Life Sciences, Department of Morphology, Tbilisi State University, Tbilisi, Georgia
| | | | - Christine Terryn
- Platform of Cell and Tissue Imaging (PICT), Université de Reims Champagne Ardenne
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Rodríguez-Ulloa A, Ramos Y, Sánchez-Puente A, Perera Y, Musacchio-Lasa A, Fernández-de-Cossio J, Padrón G, López LJ, Besada V, Perea SE. The Combination of the CIGB-300 Anticancer Peptide and Cisplatin Modulates Proteins Related to Cell Survival, DNA Repair and Metastasis in a Lung Cancer Cell Line Model. CURR PROTEOMICS 2019. [DOI: 10.2174/1570164616666190126104325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
CIGB-300 is a pro-apoptotic peptide that abrogates CK2-mediated phosphorylation,
and can elicit synergistic interaction in vitro and in vivo when combined with certain anticancer
drugs.
Objective:
The combination of CIGB-300 with cisplatin is studied through data mining and expressionbased
proteomics to reveal the molecular basis of this interaction. Cisplatin resistance-associated proteins,
which have also been reported as CK2 substrates, were first identified by bioinformatic analyses.
Methods:
Data from these analyses suggested that the cisplatin resistance phenotype could be directly
improved by inhibiting CK2 phosphorylation on specific substrates. Furthermore, 157 proteins were
differentially modulated on the NCI-H125 lung cancer cell line in response to CIGB-300, cisplatin or
both drugs as determined by LC-MS/MS.
Results:
The expression of 28 cisplatin resistance-associated proteins was changed when cisplatin was
combined with CIGB-300. Overall, the proteins identified are also related to cell survival, cell proliferation
and metastasis. Furthermore, the CIGB-300 regulated proteome revealed proteins that were initially
involved in the mechanism of action of CIGB-300 and cisplatin as single agents.
Conclusion:
This is the first report describing the protein array modulated by combining CIGB-300
and cisplatin that will support the rationale for future clinical settings based on a multi-target cancer
therapy.
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Affiliation(s)
| | - Yassel Ramos
- Department of Proteomics, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Aniel Sánchez-Puente
- Department of Proteomics, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Yasser Perera
- Laboratory of Molecular Oncology, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Alexis Musacchio-Lasa
- Department of Bioinformatics, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | | | - Gabriel Padrón
- Department of Proteomics, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Luis J.G. López
- Department of Proteomics, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Vladimir Besada
- Department of Proteomics, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Silvio E. Perea
- Laboratory of Molecular Oncology, Center for Genetic Engineering and Biotechnology, Havana, Cuba
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Hoque A, Williamson NA, Ameen SS, Ciccotosto GD, Hossain MI, Oakhill JS, Ng DCH, Ang CS, Cheng HC. Quantitative proteomic analyses of dynamic signalling events in cortical neurons undergoing excitotoxic cell death. Cell Death Dis 2019; 10:213. [PMID: 30824683 PMCID: PMC6397184 DOI: 10.1038/s41419-019-1445-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 01/20/2019] [Accepted: 02/01/2019] [Indexed: 12/23/2022]
Abstract
Excitotoxicity, caused by overstimulation or dysregulation of ionotropic glutamate receptors (iGluRs), is a pathological process directing neuronal death in many neurological disorders. The aberrantly stimulated iGluRs direct massive influx of calcium ions into the affected neurons, leading to changes in expression and phosphorylation of specific proteins to modulate their functions and direct their participation in the signalling pathways that induce excitotoxic neuronal death. To define these pathways, we used quantitative proteomic approaches to identify these neuronal proteins (referred to as the changed proteins) and determine how their expression and/or phosphorylation dynamically changed in association with excitotoxic cell death. Our data, available in ProteomeXchange with identifier PXD008353, identified over 100 changed proteins exhibiting significant alterations in abundance and/or phosphorylation levels at different time points (5–240 min) in neurons after glutamate overstimulation. Bioinformatic analyses predicted that many of them are components of signalling networks directing defective neuronal morphology and functions. Among them, the well-known neuronal survival regulators including mitogen-activated protein kinases Erk1/2, glycogen synthase kinase 3 (GSK3) and microtubule-associated protein (Tau), were selected for validation by biochemical approaches, which confirmed the findings of the proteomic analysis. Bioinformatic analysis predicted Protein Kinase B (Akt), c-Jun kinase (JNK), cyclin-dependent protein kinase 5 (Cdk5), MAP kinase kinase (MEK), Casein kinase 2 (CK2), Rho-activated protein kinase (Rock) and Serum/glucocorticoid-regulated kinase 1 (SGK1) as the potential upstream kinases phosphorylating some of the changed proteins. Further biochemical investigation confirmed the predictions of sustained changes of the activation states of neuronal Akt and CK2 in excitotoxicity. Thus, future investigation to define the signalling pathways directing the dynamic alterations in abundance and phosphorylation of the identified changed neuronal proteins will help elucidate the molecular mechanism of neuronal death in excitotoxicity.
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Affiliation(s)
- Ashfaqul Hoque
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Cell Signalling Research Laboratories, University of Melbourne, Parkville, VIC, 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia.,Metabolic Signalling Laboratory, St. Vincent's Institute for Medical Research, University of Melbourne, Fitzroy, VIC, 3065, Australia
| | - Nicholas A Williamson
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - S Sadia Ameen
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Cell Signalling Research Laboratories, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Giuseppe D Ciccotosto
- Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, VIC, 3010, Australia
| | - M Iqbal Hossain
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jonathan S Oakhill
- Metabolic Signalling Laboratory, St. Vincent's Institute for Medical Research, University of Melbourne, Fitzroy, VIC, 3065, Australia.,Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Victoria, 3000, Australia
| | - Dominic C H Ng
- School of Biomedical Sciences, University of Queensland, St. Lucia, QLD, Australia
| | - Ching-Seng Ang
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Heung-Chin Cheng
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia. .,Cell Signalling Research Laboratories, University of Melbourne, Parkville, VIC, 3010, Australia. .,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia.
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45
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Phosphoregulated FMRP phase separation models activity-dependent translation through bidirectional control of mRNA granule formation. Proc Natl Acad Sci U S A 2019; 116:4218-4227. [PMID: 30765518 DOI: 10.1073/pnas.1814385116] [Citation(s) in RCA: 215] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Activity-dependent translation requires the transport of mRNAs within membraneless protein assemblies known as neuronal granules from the cell body toward synaptic regions. Translation of mRNA is inhibited in these granules during transport but quickly activated in response to neuronal stimuli at the synapse. This raises an important question: how does synaptic activity trigger translation of once-silenced mRNAs? Here, we demonstrate a strong connection between phase separation, the process underlying the formation of many different types of cellular granules, and in vitro inhibition of translation. By using the Fragile X Mental Retardation Protein (FMRP), an abundant neuronal granule component and translational repressor, we show that FMRP phase separates in vitro with RNA into liquid droplets mediated by its C-terminal low-complexity disordered region (i.e., FMRPLCR). FMRPLCR posttranslational modifications by phosphorylation and methylation have opposing effects on in vitro translational regulation, which corroborates well with their critical concentrations for phase separation. Our results, combined with bioinformatics evidence, are supportive of phase separation as a general mechanism controlling activity-dependent translation.
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Forget A, Martignetti L, Puget S, Calzone L, Brabetz S, Picard D, Montagud A, Liva S, Sta A, Dingli F, Arras G, Rivera J, Loew D, Besnard A, Lacombe J, Pagès M, Varlet P, Dufour C, Yu H, Mercier AL, Indersie E, Chivet A, Leboucher S, Sieber L, Beccaria K, Gombert M, Meyer FD, Qin N, Bartl J, Chavez L, Okonechnikov K, Sharma T, Thatikonda V, Bourdeaut F, Pouponnot C, Ramaswamy V, Korshunov A, Borkhardt A, Reifenberger G, Poullet P, Taylor MD, Kool M, Pfister SM, Kawauchi D, Barillot E, Remke M, Ayrault O. Aberrant ERBB4-SRC Signaling as a Hallmark of Group 4 Medulloblastoma Revealed by Integrative Phosphoproteomic Profiling. Cancer Cell 2018; 34:379-395.e7. [PMID: 30205043 DOI: 10.1016/j.ccell.2018.08.002] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 05/12/2018] [Accepted: 08/03/2018] [Indexed: 12/20/2022]
Abstract
The current consensus recognizes four main medulloblastoma subgroups (wingless, Sonic hedgehog, group 3 and group 4). While medulloblastoma subgroups have been characterized extensively at the (epi-)genomic and transcriptomic levels, the proteome and phosphoproteome landscape remain to be comprehensively elucidated. Using quantitative (phospho)-proteomics in primary human medulloblastomas, we unravel distinct posttranscriptional regulation leading to highly divergent oncogenic signaling and kinase activity profiles in groups 3 and 4 medulloblastomas. Specifically, proteomic and phosphoproteomic analyses identify aberrant ERBB4-SRC signaling in group 4. Hence, enforced expression of an activated SRC combined with p53 inactivation induces murine tumors that resemble group 4 medulloblastoma. Therefore, our integrative proteogenomics approach unveils an oncogenic pathway and potential therapeutic vulnerability in the most common medulloblastoma subgroup.
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Affiliation(s)
- Antoine Forget
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France.
| | - Loredana Martignetti
- Institut Curie, 26 rue d'Ulm, 75005 Paris, France; PSL Research University, 75005 Paris, France; Inserm, U900, 75005 Paris, France; Mines Paris Tech, 77305 cedex Fontainebleau, France
| | - Stéphanie Puget
- Department of Pediatric Neurosurgery, Necker University Hospital, University Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Laurence Calzone
- Institut Curie, 26 rue d'Ulm, 75005 Paris, France; PSL Research University, 75005 Paris, France; Inserm, U900, 75005 Paris, France; Mines Paris Tech, 77305 cedex Fontainebleau, France
| | - Sebastian Brabetz
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Daniel Picard
- Department of Pediatric Neuro-Oncogenomics, DKFZ, Heidelberg, Germany; Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany; Institute of Neuropathology, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany; DKTK, Partner Site, Essen/Düsseldorf, Germany
| | - Arnau Montagud
- Institut Curie, 26 rue d'Ulm, 75005 Paris, France; PSL Research University, 75005 Paris, France; Inserm, U900, 75005 Paris, France; Mines Paris Tech, 77305 cedex Fontainebleau, France
| | - Stéphane Liva
- Institut Curie, 26 rue d'Ulm, 75005 Paris, France; PSL Research University, 75005 Paris, France; Inserm, U900, 75005 Paris, France; Mines Paris Tech, 77305 cedex Fontainebleau, France
| | - Alexandre Sta
- Institut Curie, 26 rue d'Ulm, 75005 Paris, France; PSL Research University, 75005 Paris, France; Inserm, U900, 75005 Paris, France; Mines Paris Tech, 77305 cedex Fontainebleau, France
| | - Florent Dingli
- Proteomics and Mass Spectrometry Laboratory, Institut Curie, PSL Research University, 75005 Paris, France
| | - Guillaume Arras
- Proteomics and Mass Spectrometry Laboratory, Institut Curie, PSL Research University, 75005 Paris, France
| | - Jaime Rivera
- Proteomics and Mass Spectrometry Laboratory, Institut Curie, PSL Research University, 75005 Paris, France
| | - Damarys Loew
- Proteomics and Mass Spectrometry Laboratory, Institut Curie, PSL Research University, 75005 Paris, France
| | - Aurore Besnard
- Department of Neuropathology, Sainte-Anne Hospital, 75014 Paris, France; University Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Joëlle Lacombe
- Department of Neuropathology, Sainte-Anne Hospital, 75014 Paris, France; University Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Mélanie Pagès
- Department of Neuropathology, Sainte-Anne Hospital, 75014 Paris, France; University Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Pascale Varlet
- Department of Neuropathology, Sainte-Anne Hospital, 75014 Paris, France; University Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Christelle Dufour
- Department of Pediatric and Adolescent Oncology, Gustave Roussy, Rue Edouard Vaillant, 94805 Villejuif, France
| | - Hua Yu
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
| | - Audrey L Mercier
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
| | - Emilie Indersie
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
| | - Anaïs Chivet
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
| | - Sophie Leboucher
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France; Institut Curie, Centre de Recherche, Plateforme d'Histologie, Orsay 91405, France
| | - Laura Sieber
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kevin Beccaria
- Department of Pediatric Neurosurgery, Necker University Hospital, University Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Michael Gombert
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Frauke D Meyer
- Department of Pediatric Neuro-Oncogenomics, DKFZ, Heidelberg, Germany; Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany; Institute of Neuropathology, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany; DKTK, Partner Site, Essen/Düsseldorf, Germany
| | - Nan Qin
- Department of Pediatric Neuro-Oncogenomics, DKFZ, Heidelberg, Germany; Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany; Institute of Neuropathology, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany; DKTK, Partner Site, Essen/Düsseldorf, Germany
| | - Jasmin Bartl
- Department of Pediatric Neuro-Oncogenomics, DKFZ, Heidelberg, Germany; Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany; Institute of Neuropathology, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany; DKTK, Partner Site, Essen/Düsseldorf, Germany
| | - Lukas Chavez
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Tanvi Sharma
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Venu Thatikonda
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Franck Bourdeaut
- Paris-Sciences-Lettres Research University, Institut Curie Research Center, SiRIC, Laboratory of Translational Research in Pediatric Oncology, Paris 75005, France; Paris-Sciences-Lettres Research University, Institut Curie Research Center, INSERM U830, Laboratory of Biology and Genetics of Cancers, Paris 75005, France
| | - Celio Pouponnot
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
| | - Vijay Ramaswamy
- Division of Haematology/Oncology, Hospital for Sick Children and Department of Paediatrics, Hospital for Sick Children, Toronto, ON, Canada
| | - Andrey Korshunov
- Clinical Cooperation Unit Neuropathology (G380), German Cancer Research Center (DKFZ), and Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Guido Reifenberger
- Institute of Neuropathology, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Patrick Poullet
- Institut Curie, 26 rue d'Ulm, 75005 Paris, France; PSL Research University, 75005 Paris, France; Inserm, U900, 75005 Paris, France; Mines Paris Tech, 77305 cedex Fontainebleau, France
| | - Michael D Taylor
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON, Canada; Departments of Surgery, Laboratory Medicine and Pathobiology, and Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Marcel Kool
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany; Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Daisuke Kawauchi
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany.
| | - Emmanuel Barillot
- Institut Curie, 26 rue d'Ulm, 75005 Paris, France; PSL Research University, 75005 Paris, France; Inserm, U900, 75005 Paris, France; Mines Paris Tech, 77305 cedex Fontainebleau, France.
| | - Marc Remke
- Department of Pediatric Neuro-Oncogenomics, DKFZ, Heidelberg, Germany; Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany; Institute of Neuropathology, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany; DKTK, Partner Site, Essen/Düsseldorf, Germany.
| | - Olivier Ayrault
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France.
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47
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Werner A, Baur R, Teerikorpi N, Kaya DU, Rape M. Multisite dependency of an E3 ligase controls monoubiquitylation-dependent cell fate decisions. eLife 2018; 7:35407. [PMID: 29999490 PMCID: PMC6057744 DOI: 10.7554/elife.35407] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 07/07/2018] [Indexed: 12/31/2022] Open
Abstract
Metazoan development depends on tightly regulated gene expression programs that instruct progenitor cells to adopt specialized fates. Recent work found that posttranslational modifications, such as monoubiquitylation, can determine cell fate also independently of effects on transcription, yet how monoubiquitylation is implemented during development is poorly understood. Here, we have identified a regulatory circuit that controls monoubiquitylation-dependent neural crest specification by the E3 ligase CUL3 and its substrate adaptor KBTBD8. We found that CUL3KBTBD8 monoubiquitylates its essential targets only after these have been phosphorylated in multiple motifs by CK2, a kinase whose levels gradually increase during embryogenesis. Its dependency on multisite phosphorylation allows CUL3KBTBD8 to convert the slow rise in embryonic CK2 into decisive recognition of ubiquitylation substrates, which in turn is essential for neural crest specification. We conclude that multisite dependency of an E3 ligase provides a powerful mechanism for switch-like cell fate transitions controlled by monoubiquitylation.
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Affiliation(s)
- Achim Werner
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Regina Baur
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Nia Teerikorpi
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Deniz U Kaya
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Michael Rape
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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48
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Franchin C, Borgo C, Cesaro L, Zaramella S, Vilardell J, Salvi M, Arrigoni G, Pinna LA. Re-evaluation of protein kinase CK2 pleiotropy: new insights provided by a phosphoproteomics analysis of CK2 knockout cells. Cell Mol Life Sci 2018; 75:2011-2026. [PMID: 29119230 PMCID: PMC11105740 DOI: 10.1007/s00018-017-2705-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/28/2017] [Accepted: 10/30/2017] [Indexed: 10/18/2022]
Abstract
CK2 denotes a ubiquitous and pleiotropic protein kinase whose holoenzyme is composed of two catalytic (α and/or α') and two regulatory β subunits. The CK2 consensus sequence, S/T-x-x-D/E/pS/pT is present in numerous phosphosites, but it is not clear how many of these are really generated by CK2. To gain information about this issue, advantage has been taken of C2C12 cells entirely deprived of both CK2 catalytic subunits by the CRISPR/Cas9 methodology. A comparative SILAC phosphoproteomics analysis reveals that, although about 30% of the quantified phosphosites do conform to the CK2 consensus, only one-third of these are substantially reduced in the CK2α/α'(-/-) cells, consistent with their generation by CK2. A parallel study with C2C12 cells deprived of the regulatory β subunit discloses a role of this subunit in determining CK2 targeting. We also find that phosphosites notoriously generated by CK2 are not fully abrogated in CK2α/α'(-/-) cells, while some phosphosites unrelated to CK2 are significantly altered. Collectively taken our data allow to conclude that the phosphoproteome generated by CK2 is not as ample and rigidly pre-determined as it was believed before. They also show that the lack of CK2 promotes phosphoproteomics perturbations attributable to kinases other than CK2.
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Affiliation(s)
- Cinzia Franchin
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padua, Italy
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Via G. Orus 2/B, Padua, Italy
| | - Christian Borgo
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padua, Italy
| | - Luca Cesaro
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Via G. Orus 2/B, Padua, Italy
| | - Silvia Zaramella
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padua, Italy
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Via G. Orus 2/B, Padua, Italy
| | - Jordi Vilardell
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padua, Italy
| | - Mauro Salvi
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padua, Italy.
| | - Giorgio Arrigoni
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padua, Italy.
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Via G. Orus 2/B, Padua, Italy.
| | - Lorenzo A Pinna
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padua, Italy.
- CNR Institute of Neurosciences, Via U. Bassi 58/B, Padua, Italy.
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49
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Perea SE, Baladrón I, Valenzuela C, Perera Y. CIGB-300: A peptide-based drug that impairs the Protein Kinase CK2-mediated phosphorylation. Semin Oncol 2018; 45:58-67. [PMID: 30318085 DOI: 10.1053/j.seminoncol.2018.04.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 04/20/2018] [Indexed: 01/09/2023]
Abstract
Protein kinase CK2, formerly referred to as casein kinase II, is a serine/threonine kinase often found overexpressed in solid tumors and hematologic malignancies that phosphorylates many substrates integral to the hallmarks of cancer. CK2 has emerged as a viable oncology target having been experimentally validated with different kinase inhibitors, including small molecule ATP-competitors, synthetic peptides, and antisense oligonucleotides. To date only two CK2 inhibitors, CIGB-300 and CX-4945, have entered the clinic in phase 1-2 trials. This review provides information on CIGB-300, a cell-permeable cyclic peptide that inhibits CK2-mediated phosphorylation by targeting the substrate phosphoacceptor domain. We review data that support the concept of CK2 as an anticancer target, address the mechanism of action, and summarize preclinical studies showing antiangiogenic and antimetastatic effects as well as synergism with anticancer drugs in preclinical models. We also summarize early clinical research (phase 1/2 trials) of CIGB-300 in cervical cancer, including data in combination with chemoradiotherapy. The clinical data demonstrate the safety, tolerability, and clinical effects of intratumoral injections of CIGB-300 and provide the foundation for future phase 3 clinical trials in locally advanced cervical cancer in combination with standard chemoradiotherapy.
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Affiliation(s)
- Silvio E Perea
- Molecular Oncology Laboratory, Biomedical Research Area, Center for Genetic Engineering and Biotechnology, Havana, Cuba.
| | - Idania Baladrón
- Clinical Research Division, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Carmen Valenzuela
- Clinical Research Division, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Yasser Perera
- Molecular Oncology Laboratory, Biomedical Research Area, Center for Genetic Engineering and Biotechnology, Havana, Cuba
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50
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Goel RK, Paczkowska M, Reimand J, Napper S, Lukong KE. Phosphoproteomics Analysis Identifies Novel Candidate Substrates of the Nonreceptor Tyrosine Kinase, Src- related Kinase Lacking C-terminal Regulatory Tyrosine and N-terminal Myristoylation Sites (SRMS). Mol Cell Proteomics 2018; 17:925-947. [PMID: 29496907 DOI: 10.1074/mcp.ra118.000643] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Indexed: 01/23/2023] Open
Abstract
SRMS (Src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristoylation sites), also known as PTK 70 (Protein tyrosine kinase 70), is a non-receptor tyrosine kinase that belongs to the BRK family of kinases (BFKs). To date less is known about the cellular role of SRMS primarily because of the unidentified substrates or signaling intermediates regulated by the kinase. In this study, we used phosphotyrosine antibody-based immunoaffinity purification in large-scale label-free quantitative phosphoproteomics to identify novel candidate substrates of SRMS. Our analyses led to the identification of 1258 tyrosine-phosphorylated peptides which mapped to 663 phosphoproteins, exclusively from SRMS-expressing cells. DOK1, a previously characterized SRMS substrate, was also identified in our analyses. Functional enrichment analyses revealed that the candidate SRMS substrates were enriched in various biological processes including protein ubiquitination, mitotic cell cycle, energy metabolism and RNA processing, as well as Wnt and TNF signaling. Analyses of the sequence surrounding the phospho-sites in these proteins revealed novel candidate SRMS consensus substrate motifs. We utilized customized high-throughput peptide arrays to validate a subset of the candidate SRMS substrates identified in our MS-based analyses. Finally, we independently validated Vimentin and Sam68, as bona fide SRMS substrates through in vitro and in vivo assays. Overall, our study identified a number of novel and biologically relevant SRMS candidate substrates, which suggests the involvement of the kinase in a vast array of unexplored cellular functions.
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Affiliation(s)
- Raghuveera Kumar Goel
- From the ‡Department of Biochemistry, College of Medicine, 107 Wiggins Road, University of Saskatchewan, Saskatoon S7N 5E5, Saskatchewan, Canada
| | - Marta Paczkowska
- §Computational Biology Program, Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto M5G 0A3, Ontario, Canada
| | - Jüri Reimand
- §Computational Biology Program, Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto M5G 0A3, Ontario, Canada.,¶Department of Medical Biophysics, University of Toronto, 101 College Street Suite 15-701, Toronto M5G 1L7, Ontario, Canada
| | - Scott Napper
- From the ‡Department of Biochemistry, College of Medicine, 107 Wiggins Road, University of Saskatchewan, Saskatoon S7N 5E5, Saskatchewan, Canada.,‖Vaccine and Infectious Disease Organization - International Vaccine Centre (VIDO-InterVac), 120 Veterinary Road, University of Saskatchewan, Saskatoon S7N 5E3, Saskatchewan, Canada
| | - Kiven Erique Lukong
- From the ‡Department of Biochemistry, College of Medicine, 107 Wiggins Road, University of Saskatchewan, Saskatoon S7N 5E5, Saskatchewan, Canada;
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