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Can H, Chanumolu SK, Nielsen BD, Alvarez S, Naldrett MJ, Ünlü G, Otu HH. Integration of Meta-Multi-Omics Data Using Probabilistic Graphs and External Knowledge. Cells 2023; 12:1998. [PMID: 37566077 PMCID: PMC10417344 DOI: 10.3390/cells12151998] [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: 05/12/2023] [Revised: 07/11/2023] [Accepted: 08/02/2023] [Indexed: 08/12/2023] Open
Abstract
Multi-omics has the promise to provide a detailed molecular picture of biological systems. Although obtaining multi-omics data is relatively easy, methods that analyze such data have been lagging. In this paper, we present an algorithm that uses probabilistic graph representations and external knowledge to perform optimal structure learning and deduce a multifarious interaction network for multi-omics data from a bacterial community. Kefir grain, a microbial community that ferments milk and creates kefir, represents a self-renewing, stable, natural microbial community. Kefir has been shown to have a wide range of health benefits. We obtained a controlled bacterial community using the two most abundant and well-studied species in kefir grains: Lentilactobacillus kefiri and Lactobacillus kefiranofaciens. We applied growth temperatures of 30 °C and 37 °C and obtained transcriptomic, metabolomic, and proteomic data for the same 20 samples (10 samples per temperature). We obtained a multi-omics interaction network, which generated insights that would not have been possible with single-omics analysis. We identified interactions among transcripts, proteins, and metabolites, suggesting active toxin/antitoxin systems. We also observed multifarious interactions that involved the shikimate pathway. These observations helped explain bacterial adaptation to different stress conditions, co-aggregation, and increased activation of L. kefiranofaciens at 37 °C.
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Affiliation(s)
- Handan Can
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Sree K. Chanumolu
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Barbara D. Nielsen
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Sophie Alvarez
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Michael J. Naldrett
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Gülhan Ünlü
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID 83844, USA
- Department of Chemical and Biological Engineering, University of Idaho, Moscow, ID 83844, USA
- School of Food Science, Washington State University, Pullman, WA 99164, USA
| | - Hasan H. Otu
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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2
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Miranda-Galvis M, Carneiro Soares C, Moretto Carnielli C, Ramalho Buttura J, Sales de Sá R, Kaminagakura E, Marchi FA, Paes Leme AF, Lópes Pinto CA, Santos-Silva AR, Moraes Castilho R, Kowalski LP, Squarize CH. New Insights into the Impact of Human Papillomavirus on Oral Cancer in Young Patients: Proteomic Approach Reveals a Novel Role for S100A8. Cells 2023; 12:cells12091323. [PMID: 37174723 PMCID: PMC10177374 DOI: 10.3390/cells12091323] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/29/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Human papillomavirus (HPV) infection has recently been linked to a subset of cancers affecting the oral cavity. However, the molecular mechanisms underlying HPV-driven oral squamous cell carcinoma (OSCC) onset and progression are poorly understood. METHODS We performed MS-based proteomics profiling based on HPV status in OSCC in young patients, following biological characterization and cell assays to explore the proteome functional landscape. RESULTS Thirty-nine proteins are differentially abundant between HPV (+) and HPV (-) OSCC. Among them, COPS3, DYHC1, and S100A8 are unfavorable for tumor recurrence and survival, in contrast to A2M and Serpine1, low levels of which show an association with better DFS. Remarkably, S100A8 is considered an independent prognostic factor for lower survival rates, and at high levels, it alters tumor-associated immune profiling, showing a lower proportion of M1 macrophages and dendritic cells. HPV (+) OSCC also displayed the pathogen-associated patterns receptor that, when activated, triggered the S100A8 and NFκB inflammatory responses. CONCLUSION HPV (+) OSCC has a peculiar microenvironment pattern distinctive from HPV (-), involving the expression of pathogen-associated pattern receptors, S100A8 overexpression, and NFκB activation and responses, which has important consequences in prognosis and may guide therapeutic decisions.
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Affiliation(s)
- Marisol Miranda-Galvis
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA
- Oral Diagnosis Department, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba 13414-903, SP, Brazil
| | - Carolina Carneiro Soares
- Oral Diagnosis Department, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba 13414-903, SP, Brazil
- Department of Microbiology, Immune Biology, and Genetics, Center for Molecular Biology, University of Vienna, 1030 Vienna, Austria
| | - Carolina Moretto Carnielli
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil
| | - Jaqueline Ramalho Buttura
- Laboratory of Bioinformatics and Computational Biology, A.C.Camargo Cancer Center (CIPE), São Paulo 01508-010, SP, Brazil
| | - Raisa Sales de Sá
- Oral Diagnosis Department, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba 13414-903, SP, Brazil
| | - Estela Kaminagakura
- Department of Bioscience and Oral Diagnosis, Science and Technology Institute, University of São Paulo State (UNESP), São José dos Campos 01049-010, SP, Brazil
| | - Fabio Albuquerque Marchi
- Center for Translational Research in Oncology, Cancer Institute of the State of São Paulo (ICESP), São Paulo 01246-000, SP, Brazil
- Comprehensive Center for Precision Oncology, University of São Paulo, São Paulo 05508-900, SP, Brazil
| | - Adriana Franco Paes Leme
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil
| | - Clóvis A Lópes Pinto
- Department of Anatomic Pathology, A.C.Camargo Cancer Center, São Paulo 01509-001, SP, Brazil
| | - Alan Roger Santos-Silva
- Oral Diagnosis Department, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba 13414-903, SP, Brazil
| | - Rogerio Moraes Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Luiz Paulo Kowalski
- Head and Neck Surgery Department, Medical School, University of São Paulo, São Paulo 05508-900, SP, Brazil
- Department of Head and Neck Surgery and Otorhinolaryngology, A.C.Camargo Cancer Center, São Paulo 01509-001, SP, Brazil
| | - Cristiane Helena Squarize
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
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3
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Tang HW, Spirohn K, Hu Y, Hao T, Kovács IA, Gao Y, Binari R, Yang-Zhou D, Wan KH, Bader JS, Balcha D, Bian W, Booth BW, Coté AG, de Rouck S, Desbuleux A, Goh KY, Kim DK, Knapp JJ, Lee WX, Lemmens I, Li C, Li M, Li R, Lim HJ, Liu Y, Luck K, Markey D, Pollis C, Rangarajan S, Rodiger J, Schlabach S, Shen Y, Sheykhkarimli D, TeeKing B, Roth FP, Tavernier J, Calderwood MA, Hill DE, Celniker SE, Vidal M, Perrimon N, Mohr SE. Next-generation large-scale binary protein interaction network for Drosophila melanogaster. Nat Commun 2023; 14:2162. [PMID: 37061542 PMCID: PMC10105736 DOI: 10.1038/s41467-023-37876-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 04/04/2023] [Indexed: 04/17/2023] Open
Abstract
Generating reference maps of interactome networks illuminates genetic studies by providing a protein-centric approach to finding new components of existing pathways, complexes, and processes. We apply state-of-the-art methods to identify binary protein-protein interactions (PPIs) for Drosophila melanogaster. Four all-by-all yeast two-hybrid (Y2H) screens of > 10,000 Drosophila proteins result in the 'FlyBi' dataset of 8723 PPIs among 2939 proteins. Testing subsets of data from FlyBi and previous PPI studies using an orthogonal assay allows for normalization of data quality; subsequent integration of FlyBi and previous data results in an expanded binary Drosophila reference interaction network, DroRI, comprising 17,232 interactions among 6511 proteins. We use FlyBi data to generate an autophagy network, then validate in vivo using autophagy-related assays. The deformed wings (dwg) gene encodes a protein that is both a regulator and a target of autophagy. Altogether, these resources provide a foundation for building new hypotheses regarding protein networks and function.
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Affiliation(s)
- Hong-Wen Tang
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Division of Cellular & Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, 169610, Singapore
| | - Kerstin Spirohn
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Tong Hao
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - István A Kovács
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Department of Physics and Astronomy, Northwestern University, 633 Clark Street, Evanston, IL, 60208, USA
- Northwestern Institute on Complex Systems, Chambers Hall, Northwestern University, 600 Foster St, Evanston, IL, 60208, USA
| | - Yue Gao
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Richard Binari
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Donghui Yang-Zhou
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Kenneth H Wan
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Joel S Bader
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
- High-Throughput Biology Center, Institute of Basic Biological Sciences, Johns Hopkins School of Medicine, 733 North Broadway, Baltimore, MD, 21205, USA
| | - Dawit Balcha
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Wenting Bian
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Benjamin W Booth
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Atina G Coté
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto, 160 College St, Toronto, ON, M5S 3E1, Canada
- Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health, 600 University Ave, Toronto, ON, M5G 1×5, Canada
| | - Steffi de Rouck
- Cytokine Receptor Lab, VIB Center for Medical Biotechnology, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
| | - Alice Desbuleux
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Kah Yong Goh
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Dae-Kyum Kim
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, 665 Elm St., Buffalo, NY, 14203, USA
| | - Jennifer J Knapp
- Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto, 160 College St, Toronto, ON, M5S 3E1, Canada
- Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health, 600 University Ave, Toronto, ON, M5G 1×5, Canada
| | - Wen Xing Lee
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Irma Lemmens
- Cytokine Receptor Lab, VIB Center for Medical Biotechnology, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
| | - Cathleen Li
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Mian Li
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Roujia Li
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto, 160 College St, Toronto, ON, M5S 3E1, Canada
- Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health, 600 University Ave, Toronto, ON, M5G 1×5, Canada
| | - Hyobin Julianne Lim
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, 665 Elm St., Buffalo, NY, 14203, USA
| | - Yifang Liu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Katja Luck
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Dylan Markey
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Carl Pollis
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Sudharshan Rangarajan
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Jonathan Rodiger
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Sadie Schlabach
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Yun Shen
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Dayag Sheykhkarimli
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto, 160 College St, Toronto, ON, M5S 3E1, Canada
- Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health, 600 University Ave, Toronto, ON, M5G 1×5, Canada
| | - Bridget TeeKing
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Frederick P Roth
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto, 160 College St, Toronto, ON, M5S 3E1, Canada
- Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health, 600 University Ave, Toronto, ON, M5G 1×5, Canada
- Department of Computer Science, University of Toronto, 40 St George St, Toronto, ON, M5S 2E4, Canada
| | - Jan Tavernier
- Cytokine Receptor Lab, VIB Center for Medical Biotechnology, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
| | - Michael A Calderwood
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - David E Hill
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Susan E Celniker
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA.
| | - Marc Vidal
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
- Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
| | - Stephanie E Mohr
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
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4
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de Souza LP, Fernie AR. Databases and Tools to Investigate Protein-Metabolite Interactions. Methods Mol Biol 2023; 2554:231-249. [PMID: 36178629 DOI: 10.1007/978-1-0716-2624-5_14] [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: 06/16/2023]
Abstract
Protein-metabolite interactions (PMIs) are directly responsible for the regulation of numerous processes. From the direct regulation of enzymes to complex developmental processes intermediated by hormones, PMIs are central to understanding the molecular mechanisms of important physiological phenomena. Still, proving such interactions experimentally has proven an arduous task. We discuss here some of the current technologies contributing to expand our knowledge on PMIs, with particular emphasis on platforms and databases to explore the highly heterogenous nature of characterized PMIs, which is likely to be an essential resource on the development of new computational approaches to predict and validate interactions based on large-scale PMI screenings.
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Affiliation(s)
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
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5
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Ferezin CDC, Basei FL, Melo‐Hanchuk TD, de Oliveira AL, Peres de Oliveira A, Mori MP, de Souza‐Pinto NC, Kobarg J. NEK5 interacts with LonP1 and its kinase activity is essential for the regulation of mitochondrial functions and mtDNA maintenance. FEBS Open Bio 2021; 11:546-563. [PMID: 33547867 PMCID: PMC7931231 DOI: 10.1002/2211-5463.13108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/19/2021] [Accepted: 02/04/2021] [Indexed: 12/16/2022] Open
Abstract
Little is known about Nima-related kinase (NEKs), a widely conserved family of kinases that have key roles in cell-cycle progression. Nevertheless, it is now clear that multiple NEK family members act in networks, not only to regulate specific events of mitosis, but also to regulate metabolic events independently of the cell cycle. NEK5 was shown to act in centrosome disjunction, caspase-3 regulation, myogenesis, and mitochondrial respiration. Here, we demonstrate that NEK5 interacts with LonP1, an AAA+ mitochondrial protease implicated in protein quality control and mtDNA remodeling, within the mitochondria and it might be involved in the LonP1-TFAM signaling module. Moreover, we demonstrate that NEK5 kinase activity is required for maintaining mitochondrial mass and functionality and mtDNA integrity after oxidative damage. Taken together, these results show a new role of NEK5 in the regulation of mitochondrial homeostasis and mtDNA maintenance, possibly due to its interaction with key mitochondrial proteins, such as LonP1.
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Affiliation(s)
- Camila de Castro Ferezin
- Faculdade de Ciências FarmacêuticasUniversidade Estadual de CampinasBrazil
- Instituto de BiologiaDepartamento de Bioquímica e Biologia TecidualUniversidade Estadual de CampinasBrazil
| | - Fernanda Luisa Basei
- Faculdade de Ciências FarmacêuticasUniversidade Estadual de CampinasBrazil
- Instituto de BiologiaDepartamento de Bioquímica e Biologia TecidualUniversidade Estadual de CampinasBrazil
| | | | - Ana Luisa de Oliveira
- Instituto de BiologiaDepartamento de Bioquímica e Biologia TecidualUniversidade Estadual de CampinasBrazil
| | | | - Mateus P. Mori
- Departamento de BioquímicaInstituto de QuímicaUniversidade de São PauloBrazil
| | | | - Jörg Kobarg
- Faculdade de Ciências FarmacêuticasUniversidade Estadual de CampinasBrazil
- Instituto de BiologiaDepartamento de Bioquímica e Biologia TecidualUniversidade Estadual de CampinasBrazil
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6
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Rodríguez-Vega A, Losada-Barragán M, Berbert LR, Mesquita-Rodrigues C, Bombaça ACS, Menna-Barreto R, Aquino P, Carvalho PC, Padrón G, de Jesus JB, Cuervo P. Quantitative analysis of proteins secreted by Leishmania (Viannia) braziliensis strains associated to distinct clinical manifestations of American Tegumentary Leishmaniasis. J Proteomics 2020; 232:104077. [PMID: 33309930 DOI: 10.1016/j.jprot.2020.104077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/01/2020] [Accepted: 12/06/2020] [Indexed: 12/15/2022]
Abstract
The role of Leishmania braziliensis in the development of different clinical forms of American Tegumentary Leishmaniasis (ATL) is unclear, but it has been suggested that molecules secreted/released by parasites could modulate the clinical outcome. Here, we analyzed the infection rate and cytokine profile of macrophages pretreated with the secretome of two L. braziliensis strains associated with polar clinical forms of ATL: one associated with localized self-healing cutaneous leishmaniasis (LCL) and other associated with the disseminated form (DL). Besides, we use an iTRAQ-based quantitative proteomics approach to compare the abundance of proteins secreted by those strains. In vitro infection demonstrated that pretreatment with secretome resulted in higher number of infected macrophages, as well as higher number of amastigotes per cell. Additionally, macrophages pretreated with LCL secretome exhibited a proinflammatory profile, whereas those pretreated with the DL one did not. These findings suggest that secretomes made macrophages more susceptible to infection and that molecules secreted by each strain modulate, differentially, the macrophages' cytokine profile. Indeed, proteomics analysis showed that the DL secretome is rich in molecules involved in macrophage deactivation, while is poor in proteins that activate proinflammatory pathways. Together, our results reveal new molecules that may contribute to the infection, persistence and dissemination of the parasite. SIGNIFICANCE: Leishmania braziliensis is associated to localized self-healing cutaneous lesions (LCL), disseminated leishmaniasis (DL), and mucocutaneous lesions (MCL). To understand the role of the parasite in those distinct clinical manifestations we evaluated infection rates and cytokine profiles of macrophages pre-treated with secretomes of two L. braziliensis strains associated with DL and LCL, and quantitatively compared these secretomes. The infection index of macrophages pretreated with the DL secretome was significantly higher than that exhibited by non-treated cells. Interestingly, whereas the LCL secretome stimulated a proinflammatory setting, favoring an effector cell response that would explain the proper resolution of the disease caused by this strain, the DL strain was not able to elicit such response or has mechanisms to prevent this activation. Indeed, DL secretome is rich in peptidases that may deactivate cell pathways crucial for parasite elimination, while is poor in proteins that could activate proinflammatory pathways, favoring parasite infection and persistence.
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Affiliation(s)
- Andrés Rodríguez-Vega
- Laboratório de Pesquisa em Leishmanioses, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Monica Losada-Barragán
- Grupo de Investigación en Biología Celular y Funcional e Ingeniería de Biomoléculas, Universidad Antonio Nariño, Bogotá, Colombia
| | - Luiz Ricardo Berbert
- Laboratório de Pesquisas sobre o Timo, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Camila Mesquita-Rodrigues
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | | | - Rubem Menna-Barreto
- Laboratório de Biologia Celular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Priscila Aquino
- Instituto Leônidas e Maria Deane, Fiocruz, Manaus, AM, Brazil
| | - Paulo C Carvalho
- Laboratory for Structural and Computational Proteomics, Fiocruz-Paraná, PR, Brazil
| | - Gabriel Padrón
- Laboratório de Pesquisa em Leishmanioses, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Jose Batista de Jesus
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil; Universidade Federal de São João Del Rei, São João del Rei, MG, Brazil
| | - Patricia Cuervo
- Laboratório de Pesquisa em Leishmanioses, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil.
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7
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Giovani PA, Martins L, Salmon CR, Mofatto LS, Leme AFP, Puppin-Rontani RM, Kolli TN, Foster BL, Nociti FH, Kantovitz KR. Comparative proteomic analysis of dental cementum from deciduous and permanent teeth. J Periodontal Res 2020; 56:173-185. [PMID: 33210734 DOI: 10.1111/jre.12808] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/29/2020] [Accepted: 09/16/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND OBJECTIVES Dental cementum (DC) is a mineralized tissue covering tooth roots that plays a critical role in dental attachment. Differences in deciduous vs. permanent tooth DC have not been explored. We hypothesized that proteomic analysis of DC matrix would identify compositional differences in deciduous (DecDC) vs. permanent (PermDC) cementum that might reflect physiological or pathological differences, such as root resorption that is physiological in deciduous teeth but can be pathological in the permanent dentition. METHODS Protein extracts from deciduous (n = 25) and permanent (n = 12) teeth were pooled (five pools of DecDC, five teeth each; four pools of PermDC, three teeth each). Samples were denatured, and proteins were extracted, reduced, alkylated, digested, and analyzed by liquid chromatography-mass spectrometry (LC-MS/MS). The beta-binomial statistical test was applied to normalized spectrum counts with 5% significance level to determine differentially expressed proteins. Immunohistochemistry was used to validate selected proteins. RESULTS A total of 510 proteins were identified: 123 (24.1%) exclusive to DecDC; 128 (25.1%) exclusive to PermDC; 259 (50.8%) commonly expressed in both DecDC and PermDC. Out of 60 differentially expressed proteins, 17 (28.3%) were detected in DecDC, including myeloperoxidase (MPO), whereas 43 (71.7%) were detected in PermDC, including decorin (DCN) and osteocalcin (BGLAP). Overall, Gene Ontology (GO) analysis indicated that all expressed proteins were related to GO biological processes that included localization and response to stress, and the GO molecular function of differentially expressed proteins was enriched in cell adhesion, molecular binding, cytoskeletal protein binding, structural molecular activity, and macromolecular complex binding. Immunohistochemistry confirmed the trends for selected differentially expressed proteins in human teeth. CONCLUSIONS Clear differences were found between the proteomes of DecDC and PermDC. These findings may lead to new insights into developmental differences between DecDC and PermDC, as well as to a better understanding of physiological/pathological events such as root resorption.
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Affiliation(s)
- Priscila A Giovani
- Department of Pediatric Dentistry, Piracicaba Dental School, University of Campinas, São Paulo, Brazil
| | - Luciane Martins
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, University of Campinas, São Paulo, Brazil
| | - Cristiane R Salmon
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, University of Campinas, São Paulo, Brazil
| | - Luciana S Mofatto
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Adriana F P Leme
- Brazilian Biosciences National Laboratory, LNBio, CNPEM, Campinas, São Paulo, Brazil
| | - Regina M Puppin-Rontani
- Department of Pediatric Dentistry, Piracicaba Dental School, University of Campinas, São Paulo, Brazil
| | - Tamara N Kolli
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - Brian L Foster
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - Francisco H Nociti
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, University of Campinas, São Paulo, Brazil
| | - Kamila R Kantovitz
- Department of Pediatric Dentistry, Piracicaba Dental School, University of Campinas, São Paulo, Brazil.,Department of Dental Materials, São Leopoldo Mandic Research Center, Campinas, São Paulo, Brazil
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8
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Mazandu GK, Hooper C, Opap K, Makinde F, Nembaware V, Thomford NE, Chimusa ER, Wonkam A, Mulder NJ. IHP-PING-generating integrated human protein-protein interaction networks on-the-fly. Brief Bioinform 2020; 22:5943797. [PMID: 33129201 DOI: 10.1093/bib/bbaa277] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/12/2020] [Accepted: 09/21/2020] [Indexed: 01/04/2023] Open
Abstract
Advances in high-throughput sequencing technologies have resulted in an exponential growth of publicly accessible biological datasets. In the 'big data' driven 'post-genomic' context, much work is being done to explore human protein-protein interactions (PPIs) for a systems level based analysis to uncover useful signals and gain more insights to advance current knowledge and answer specific biological and health questions. These PPIs are experimentally or computationally predicted, stored in different online databases and some of PPI resources are updated regularly. As with many biological datasets, such regular updates continuously render older PPI datasets potentially outdated. Moreover, while many of these interactions are shared between these online resources, each resource includes its own identified PPIs and none of these databases exhaustively contains all existing human PPI maps. In this context, it is essential to enable the integration of or combining interaction datasets from different resources, to generate a PPI map with increased coverage and confidence. To allow researchers to produce an integrated human PPI datasets in real-time, we introduce the integrated human protein-protein interaction network generator (IHP-PING) tool. IHP-PING is a flexible python package which generates a human PPI network from freely available online resources. This tool extracts and integrates heterogeneous PPI datasets to generate a unified PPI network, which is stored locally for further applications.
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Affiliation(s)
- Gaston K Mazandu
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI-Africa WT Centre, University of Cape Town, Health Sciences Campus. Anzio Rd, Observatory, 7925, South Africa.,African Institute for Mathematical Sciences, 5-7 Melrose Road, Muizenberg, 7945, Cape Town, South Africa.,Division of Human Genetics, Department of Pathology, University of Cape Town, Health Sciences Campus, Anzio Rd, Observatory, 7925, South Africa
| | - Christopher Hooper
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI-Africa WT Centre, University of Cape Town, Health Sciences Campus. Anzio Rd, Observatory, 7925, South Africa
| | - Kenneth Opap
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI-Africa WT Centre, University of Cape Town, Health Sciences Campus. Anzio Rd, Observatory, 7925, South Africa
| | - Funmilayo Makinde
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI-Africa WT Centre, University of Cape Town, Health Sciences Campus. Anzio Rd, Observatory, 7925, South Africa.,African Institute for Mathematical Sciences, 5-7 Melrose Road, Muizenberg, 7945, Cape Town, South Africa
| | - Victoria Nembaware
- Division of Human Genetics, Department of Pathology, University of Cape Town, Health Sciences Campus, Anzio Rd, Observatory, 7925, South Africa
| | - Nicholas E Thomford
- Division of Human Genetics, Department of Pathology, University of Cape Town, Health Sciences Campus, Anzio Rd, Observatory, 7925, South Africa.,School of Medical Sciences, University of Cape Coast, PMB, Cape Coast, Ghana
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, University of Cape Town, Health Sciences Campus, Anzio Rd, Observatory, 7925, South Africa
| | - Ambroise Wonkam
- Division of Human Genetics, Department of Pathology, University of Cape Town, Health Sciences Campus, Anzio Rd, Observatory, 7925, South Africa
| | - Nicola J Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI-Africa WT Centre, University of Cape Town, Health Sciences Campus. Anzio Rd, Observatory, 7925, South Africa
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9
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Peres de Oliveira A, Basei FL, Slepicka PF, de Castro Ferezin C, Melo-Hanchuk TD, de Souza EE, Lima TI, Dos Santos VT, Mendes D, Silveira LR, Menck CFM, Kobarg J. NEK10 interactome and depletion reveal new roles in mitochondria. Proteome Sci 2020; 18:4. [PMID: 32368190 PMCID: PMC7189645 DOI: 10.1186/s12953-020-00160-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 04/14/2020] [Indexed: 12/29/2022] Open
Abstract
Background Members of the family of NEK protein kinases (NIMA-related kinases) were described to have crucial roles in regulating different aspects of the cell cycle. NEK10 was reported to take part in the maintenance of the G2/M checkpoint after exposure to ultraviolet light. NEK1, NEK5, NEK2 and NEK4 proteins on the other hand have been linked to mitochondrial functions. Methods HEK293T cells were transfected with FLAG empty vector or FLAG-NEK10 and treated or not with Zeocin. For proteomic analysis, proteins co-precipitated with the FLAG constructs were digested by trypsin, and then analyzed via LC-MS/MS. Proteomic data retrieved were next submitted to Integrated Interactome System analysis and differentially expressed proteins were attributed to Gene Ontology biological processes and assembled in protein networks by Cytoscape. For functional, cellular and molecular analyses two stable Nek10 silenced HeLa cell clones were established. Results Here, we discovered the following possible new NEK10 protein interactors, related to mitochondrial functions: SIRT3, ATAD3A, ATAD3B, and OAT. After zeocin treatment, the spectrum of mitochondrial interactors increased by the proteins: FKBP4, TXN, PFDN2, ATAD3B, MRPL12, ATP5J, DUT, YWHAE, CS, SIRT3, HSPA9, PDHB, GLUD1, DDX3X, and APEX1. We confirmed the interaction of NEK10 and GLUD1 by proximity ligation assay and confocal microscopy. Furthermore, we demonstrated that NEK10-depleted cells showed more fragmented mitochondria compared to the control cells. The knock down of NEK10 resulted further in changes in mitochondrial reactive oxygen species (ROS) levels, decreased citrate synthase activity, and culminated in inhibition of mitochondrial respiration, affecting particularly ATP-linked oxygen consumption rate and spare capacity. NEK10 depletion also decreased the ratio of mtDNA amplification, possibly due to DNA damage. However, the total mtDNA content increased, suggesting that NEK10 may be involved in the control of mtDNA content. Conclusions Taken together these data place NEK10 as a novel regulatory player in mitochondrial homeostasis and energy metabolism.
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Affiliation(s)
- Andressa Peres de Oliveira
- 1Instituto de Biologia, Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.,2Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Fernanda Luisa Basei
- 1Instituto de Biologia, Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.,3Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Rua Cândido Portinari, 200; Cidade Universitária Zeferino Vaz; Campinas-SP; CEP, São Paulo, 13083-871 Brazil
| | - Priscila Ferreira Slepicka
- 4Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Camila de Castro Ferezin
- 1Instituto de Biologia, Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.,3Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Rua Cândido Portinari, 200; Cidade Universitária Zeferino Vaz; Campinas-SP; CEP, São Paulo, 13083-871 Brazil
| | - Talita D Melo-Hanchuk
- 1Instituto de Biologia, Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Edmarcia Elisa de Souza
- 4Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Tanes I Lima
- 5Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.,6Departamento de Bioquímica e Imunologia, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Valquiria Tiago Dos Santos
- 2Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Davi Mendes
- 2Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Leonardo Reis Silveira
- 5Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | | | - Jörg Kobarg
- 1Instituto de Biologia, Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.,3Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Rua Cândido Portinari, 200; Cidade Universitária Zeferino Vaz; Campinas-SP; CEP, São Paulo, 13083-871 Brazil
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10
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Fonseca FP, Macedo CCS, Dos Santos Costa SF, Leme AFP, Rodrigues RR, Pontes HAR, Altemani A, van Heerden WFP, Martins MD, de Almeida OP, Santos-Silva AR, Lopes MA, Vargas PA. Mass spectrometry-based proteome profile may be useful to differentiate adenoid cystic carcinoma from polymorphous adenocarcinoma of salivary glands. Oral Surg Oral Med Oral Pathol Oral Radiol 2019; 128:639-650. [PMID: 31494112 DOI: 10.1016/j.oooo.2019.07.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 06/12/2019] [Accepted: 07/24/2019] [Indexed: 11/25/2022]
Abstract
OBJECTIVE The aim of this study was to determine the proteome of adenoid cystic carcinoma (AdCC) and polymorphous adenocarcinoma (PAc) and to identify a protein signature useful in distinguishing these two neoplasms. STUDY DESIGN Ten cases of AdCC and 10 cases of PAc were microdissected for enrichment of neoplastic tissue. The samples were submitted to liquid chromatography-tandem mass spectrometry (LC-MS/MS), and the proteomics data were analyzed by using the MaxQuant software. LC-MS/MS spectra were searched against the Human UniProt database, and statistical analyses were performed with Perseus software. Bioinformatic analyses were performed by using discovery-based proteomic data on both tumors. RESULTS LC-MS/MS analysis identified 1957 proteins. The tumors shared 1590 proteins, and 261 were exclusively identified in AdCC and 106 in PAc. Clustering analysis of the statistically significant proteins clearly separated AdCC from PAc. Protein expression 10 times higher in one group than in the other led to a signature of 16 proteins-6 upregulated in AdCC and 10 in PAc. A new clustering analysis showed reverse regulation and also differentiated both tumors. CONCLUSIONS Global proteomics may be useful in discriminating these two malignant salivary neoplasms that frequently show clinical and microscopic overlaps, but additional validation studies are still necessary to determine the diagnostic potential of the protein signature obtained.
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Affiliation(s)
- Felipe Paiva Fonseca
- Department of Oral Diagnosis, Oral Pathology Division, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba, Brazil; Department of Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Carolina Carneiro Soares Macedo
- Department of Oral Diagnosis, Oral Pathology Division, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba, Brazil
| | | | - Adriana Franco Paes Leme
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, Brazil
| | - Romênia Ramos Rodrigues
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, Brazil
| | - Hélder Antônio Rebelo Pontes
- Service of Oral Pathology, João de Barros Barreto University Hospital, Federal University of Pará, Belém, Brazil
| | - Albina Altemani
- Department of Pathology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Willie F P van Heerden
- Department of Oral Pathology and Oral Biology, School of Dentistry, University of Pretoria, Pretoria, South Africa
| | - Manoela Domingues Martins
- Department of Oral Diagnosis, Oral Pathology Division, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba, Brazil; Department of Pathology, School of Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Oslei Paes de Almeida
- Department of Oral Diagnosis, Oral Pathology Division, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba, Brazil
| | - Alan Roger Santos-Silva
- Department of Oral Diagnosis, Oral Pathology Division, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba, Brazil
| | - Márcio Ajudarte Lopes
- Department of Oral Diagnosis, Oral Pathology Division, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba, Brazil
| | - Pablo Agustin Vargas
- Department of Oral Diagnosis, Oral Pathology Division, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba, Brazil; Department of Oral Pathology and Oral Biology, School of Dentistry, University of Pretoria, Pretoria, South Africa.
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11
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Losada-Barragán M, Umaña-Pérez A, Rodriguez-Vega A, Cuervo-Escobar S, Azevedo R, Morgado FN, de Frias Carvalho V, Aquino P, Carvalho PC, Porrozzi R, Sánchez-Gómez M, Padron G, Cuervo P. Proteomic profiling of splenic interstitial fluid of malnourished mice infected with Leishmania infantum reveals defects on cell proliferation and pro-inflammatory response. J Proteomics 2019; 208:103492. [DOI: 10.1016/j.jprot.2019.103492] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/14/2019] [Accepted: 08/16/2019] [Indexed: 12/31/2022]
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12
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Sharma N, Arrigoni G, Ebinezer LB, Trentin AR, Franchin C, Giaretta S, Carletti P, Thiele-Bruhn S, Ghisi R, Masi A. A proteomic and biochemical investigation on the effects of sulfadiazine in Arabidopsis thaliana. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 178:146-158. [PMID: 31002969 DOI: 10.1016/j.ecoenv.2019.04.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/26/2019] [Accepted: 04/03/2019] [Indexed: 06/09/2023]
Abstract
Animal manure or bio-solids used as fertilizers are the main routes of antibiotic exposure in the agricultural land, which can have immense detrimental effects on plants. Sulfadiazine (SDZ), belonging to the class of sulfonamides, is one of the most detected antibiotics in the agricultural soil. In this study, the effect of SDZ on the growth, changes in antioxidant metabolite content and enzyme activities related to oxidative stress were analysed. Moreover, the proteome alterations in Arabidopsis thaliana roots in response to SDZ was examined by means of a combined iTRAQ-LC-MS/MS quantitative proteomics approach. A dose-dependent decrease in leaf biomass and root length was evidenced in response to SDZ. Increased malondialdehyde content at higher concentration (2 μM) of SDZ indicated increased lipid peroxidation and suggest the induction of oxidative stress. Glutathione levels were significantly higher compared to control, whereas there was no increase in ascorbate content or the enzyme activities of glutathione metabolism, even at higher concentrations. In total, 48 differentially abundant proteins related to stress/stimuli response followed by transcription and translation, metabolism, transport and other functions were identified. Several proteins related to oxidative, dehydration, salinity and heavy metal stresses were represented. Upregulation of peroxidases was validated with total peroxidase activity. Pathway analysis provided an indication of increased phenylpropanoid biosynthesis. Probable molecular mechanisms altered in response to SDZ are highlighted.
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Affiliation(s)
- Nisha Sharma
- DAFNAE, University of Padova, Viale Università 16, 30520 Legnaro, PD, Italy
| | - Giorgio Arrigoni
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy; Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Italy
| | | | - Anna Rita Trentin
- DAFNAE, University of Padova, Viale Università 16, 30520 Legnaro, PD, Italy
| | - Cinzia Franchin
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy; Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Italy
| | - Sabrina Giaretta
- DAFNAE, University of Padova, Viale Università 16, 30520 Legnaro, PD, Italy
| | - Paolo Carletti
- DAFNAE, University of Padova, Viale Università 16, 30520 Legnaro, PD, Italy
| | - Sören Thiele-Bruhn
- Soil Science, Trier University, Behringstraße 21, D-54286, Trier, Germany
| | - Rossella Ghisi
- DAFNAE, University of Padova, Viale Università 16, 30520 Legnaro, PD, Italy
| | - Antonio Masi
- DAFNAE, University of Padova, Viale Università 16, 30520 Legnaro, PD, Italy
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13
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Taiete T, Casati MZ, Martins L, Andia DC, Mofatto LS, Coletta RD, Monteiro MF, Araújo CF, Santamaria MP, Corrêa MG, Sallum EA, Nociti FH, Casarin RC. Novel rare frameshift variation in aggressive periodontitis: Exomic and familial-screening analysis. J Periodontol 2019; 91:263-273. [PMID: 31373687 DOI: 10.1002/jper.19-0182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/16/2019] [Accepted: 06/27/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND Aggressive periodontitis (AgP), currently periodontitis grade C, presents early onset, rapid progression, and a poorly established genetic association. Thus, this study aimed to identify genetic variants associated with AgP via whole exome sequencing (WES) through a familial screening approach. METHODS WES was performed in two nuclear families, including a proband and a parent affected by AgP and an unaffected parent and sibling. Common variants among affected individuals, excluding those common to healthy people, from each family, composed the data set associated with AgP. In silico analysis evaluated the impact of each variant on protein structure and protein-protein interactions. Moreover, identified deleterious variants were validated in a populational analysis (n = 96). RESULTS The missense single nucleotide variations (SNVs) rs142548867 in EEFSEC (c.668C>T), rs574301770 in ZNF136 (c.466C>G), and rs72821893 in KRT25 (c.800G>A) and the frameshift indels rs37146475 in GPRC6A (c.2323-2324insT) and c.1366_1372insGGAGCAG in ELN were identified in AgP and have a predicted functional impact on proteins. In silico analysis indicated that the indel in GPRC6A generates a loss of the C-terminal tail of the Gprca protein. Furthermore, this SNV was significantly associated with AgP in a population-based investigation. CONCLUSION Novel frameshift variation in GPRC6A (c.2323-2324insT) was identified as a potential genetic alteration associated with AgP occurrence.
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Affiliation(s)
- Tiago Taiete
- Department of Prosthodontics and Periodontics, Periodontics Division, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil.,Department of Dentistry, University of Araras, Araras, SP, Brazil
| | - Marcio Z Casati
- Department of Prosthodontics and Periodontics, Periodontics Division, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil.,Department of Periodontics, Paulista University, São Paulo, SP, Brazil
| | - Luciane Martins
- Department of Prosthodontics and Periodontics, Periodontics Division, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Denise C Andia
- Department of Prosthodontics and Periodontics, Periodontics Division, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil.,Dental Research Division, School of Dentistry, Paulista University, São Paulo, SP, Brazil
| | - Luciana S Mofatto
- Department of Genetics, Evolution and Bioagents, Genomic and Expression Laboratory, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - Ricardo D Coletta
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, SP, Brazil
| | - Mabelle F Monteiro
- Department of Prosthodontics and Periodontics, Periodontics Division, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Cássia F Araújo
- Department of Diagnosis and Surgery, School of Dentistry, State University of São Paulo (UNESP), São José dos Campos, Brazil
| | - Mauro P Santamaria
- Department of Diagnosis and Surgery, School of Dentistry, State University of São Paulo (UNESP), São José dos Campos, Brazil
| | - Mônica G Corrêa
- Dental Research Division, School of Dentistry, Paulista University, São Paulo, SP, Brazil
| | - Enilson A Sallum
- Department of Prosthodontics and Periodontics, Periodontics Division, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Francisco H Nociti
- Department of Prosthodontics and Periodontics, Periodontics Division, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Renato C Casarin
- Department of Prosthodontics and Periodontics, Periodontics Division, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
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14
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Zandonadi FS, Castañeda Santa Cruz E, Korvala J. New SDC function prediction based on protein-protein interaction using bioinformatics tools. Comput Biol Chem 2019; 83:107087. [PMID: 31351242 DOI: 10.1016/j.compbiolchem.2019.107087] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 05/13/2019] [Accepted: 06/23/2019] [Indexed: 12/11/2022]
Abstract
The precise roles for SDC have been complex to specify. Assigning and reanalyzing protein and peptide identification to novel protein functions is one of the most important challenges in postgenomic era. Here, we provide SDC molecular description to support, contextualize and reanalyze the corresponding protein-protein interaction (PPI). From SDC-1 data mining, we discuss the potential of bioinformatics tools to predict new biological rules of SDC. Using these methods, we have assembled new possibilities for SDC biology from PPI data, once, the understanding of biology complexity cannot be capture from one simple question.
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Affiliation(s)
- Flávia S Zandonadi
- Laboratory of Bioanalytics and Integrated Omics (LaBIOmics), Departamento de Química Analítica, Universidade de Campinas, UNICAMP, Campinas, SP, Brazil.
| | - Elisa Castañeda Santa Cruz
- Laboratory of Bioanalytics and Integrated Omics (LaBIOmics), Departamento de Química Analítica, Universidade de Campinas, UNICAMP, Campinas, SP, Brazil
| | - Johanna Korvala
- Cancer and Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, University of Oulu, Oulu, Finland
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15
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Losada-Barragán M, Umaña-Pérez A, Durães J, Cuervo-Escobar S, Rodríguez-Vega A, Ribeiro-Gomes FL, Berbert LR, Morgado F, Porrozzi R, Mendes-da-Cruz DA, Aquino P, Carvalho PC, Savino W, Sánchez-Gómez M, Padrón G, Cuervo P. Thymic Microenvironment Is Modified by Malnutrition and Leishmania infantum Infection. Front Cell Infect Microbiol 2019; 9:252. [PMID: 31355153 PMCID: PMC6639785 DOI: 10.3389/fcimb.2019.00252] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/28/2019] [Indexed: 01/23/2023] Open
Abstract
Detrimental effects of malnutrition on immune responses to pathogens have long been recognized and it is considered a main risk factor for various infectious diseases, including visceral leishmaniasis (VL). Thymus is a target of both malnutrition and infection, but its role in the immune response to Leishmania infantum in malnourished individuals is barely studied. Because we previously observed thymic atrophy and significant reduction in cellularity and chemokine levels in malnourished mice infected with L. infantum, we postulated that the thymic microenvironment is severely compromised in those animals. To test this, we analyzed the microarchitecture of the organ and measured the protein abundance in its interstitial space in malnourished BALB/c mice infected or not with L. infantum. Malnourished-infected animals exhibited a significant reduction of the thymic cortex:medulla ratio and altered abundance of proteins secreted in the thymic interstitial fluid. Eighty-one percent of identified proteins are secreted by exosomes and malnourished-infected mice showed significant decrease in exosomal proteins, suggesting that exosomal carrier system, and therefore intrathymic communication, is dysregulated in those animals. Malnourished-infected mice also exhibited a significant increase in the abundance of proteins involved in lipid metabolism and tricarboxylic acid cycle, suggestive of a non-proliferative microenvironment. Accordingly, flow cytometry analysis revealed decreased proliferation of single positive and double positive T cells in those animals. Together, the reduced cortical area, decreased proliferation, and altered protein abundance suggest a dysfunctional thymic microenvironment where T cell migration, proliferation, and maturation are compromised, contributing for the thymic atrophy observed in malnourished animals. All these alterations could affect the control of the local and systemic infection, resulting in an impaired response to L. infantum infection.
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Affiliation(s)
- Monica Losada-Barragán
- Laboratório de Pesquisa em Leishmanioses, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.,Grupo de Investigación en Biología Celular y Funcional e Ingeniería de Biomoléculas, Departamento de Biologia, Universidad Antonio Nariño, Bogotá, Colombia
| | - Adriana Umaña-Pérez
- Grupo de Investigación en Hormonas, Departamento de Química, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Jonathan Durães
- Laboratório de Pesquisa em Leishmanioses, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Sergio Cuervo-Escobar
- Facultad de Ciencias, Universidad de Ciencias Aplicadas y Ambientales, Bogotá, Colombia
| | - Andrés Rodríguez-Vega
- Laboratório de Pesquisa em Leishmanioses, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Flávia L Ribeiro-Gomes
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Luiz R Berbert
- Laboratório de Pesquisas sobre o Timo, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Fernanda Morgado
- Laboratório de Pesquisa em Leishmanioses, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Renato Porrozzi
- Laboratório de Pesquisa em Leishmanioses, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Daniella Arêas Mendes-da-Cruz
- Laboratório de Pesquisas sobre o Timo, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.,Instituto Nacional de Ciência e Tecnologia em Neuroimunomodulação, Fiocruz, Rio de Janeiro, Brazil
| | | | - Paulo C Carvalho
- Computational Mass Spectrometry and Proteomics Group, Fiocruz, Rio de Janeiro, Brazil
| | - Wilson Savino
- Laboratório de Pesquisas sobre o Timo, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.,Instituto Nacional de Ciência e Tecnologia em Neuroimunomodulação, Fiocruz, Rio de Janeiro, Brazil
| | - Myriam Sánchez-Gómez
- Grupo de Investigación en Hormonas, Departamento de Química, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Gabriel Padrón
- Laboratório de Pesquisa em Leishmanioses, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Patricia Cuervo
- Laboratório de Pesquisa em Leishmanioses, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
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Giovani PA, Salmon CR, Martins L, Leme AFP, Puppin-Rontani RM, Mofatto LS, Nociti FH, Kantovitz KR. Membrane proteome characterization of periodontal ligament cell sets from deciduous and permanent teeth. J Periodontol 2018; 90:775-787. [PMID: 30499115 DOI: 10.1002/jper.18-0217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 09/24/2018] [Accepted: 09/30/2018] [Indexed: 01/09/2023]
Abstract
BACKGROUND Physiological roles for the periodontal ligament (PDL) include tooth eruption and anchorage, force absorption, and provision of proprioceptive information. Despite the advances in understanding the biology of PDL cells, there is a lack of information regarding the molecular signature of deciduous (DecPDL) and permanent (PermPDL) PDL tissues. Thus, the present study was designed to characterize the membrane proteome of DecPDL and PermPDL cells. METHODS Primary PDL cells were obtained (n = 6) and a label-free quantitative proteome of cell membrane-enriched components was performed. Proteome findings were validated by quantitative polymerase chain reaction and Western blot assays in fresh human tissues (n = 8) and primary cell cultures (n = 6). In addition, confocal microscopy was used to verify the expression of target factors in the PDL cell cultures. RESULTS Comparative gene ontology enrichment analysis evidenced that most stickling differences involved "endomembrane system" (PICALM, STX4, and LRP10), "hydrolase activity" (NCSTN and XRCC6), "protein binding" (PICALM, STX4, GPNMB, VASP, extended-synaptotagmin 2 [ESYT2], and leucine-rich repeat containing 15 [LRRC15]), and "isomerase activity" (FKBP8). Data are available via ProteomeXchange with identifier PXD010226. At the transcript level, high PICALM in DecPDL and ESYT2 and LRRC15 in PermPDL were confirmed in fresh PDL tissues. Furthermore, Western blot analysis confirmed increased levels of PICALM, LRRC15, and ESYT2 in cells and/or fresh tissues, and confocal microscopy confirmed the trends for PICALM and LRRC15 expression in PDL cells. CONCLUSION We report the first comprehensive characterization of the membrane protein machinery of DecPDL and PermPDL cells, and together, we identified a distinct molecular signature for these cell populations, including unique proteins for DecPDL and PermPDL.
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Affiliation(s)
- Priscila A Giovani
- Department of Pediatric Dentistry, Piracicaba Dental School, University of Campinas, Campinas, São Paulo, Brazil
| | - Cristiane R Salmon
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Luciane Martins
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Adriana F P Leme
- Brazilian Biosciences National Laboratory, LNBio, CNPEM, Campinas, São Paulo, Brazil
| | - Regina M Puppin-Rontani
- Department of Pediatric Dentistry, Piracicaba Dental School, University of Campinas, Campinas, São Paulo, Brazil
| | - Luciana S Mofatto
- Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Francisco H Nociti
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Kamila R Kantovitz
- Department of Pediatric Dentistry, Piracicaba Dental School, University of Campinas, Campinas, São Paulo, Brazil.,Department of Dental Materials, São Leopoldo Mandic Research Center, Campinas, São Paulo, Brazil
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17
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Roomi S, Masi A, Conselvan GB, Trevisan S, Quaggiotti S, Pivato M, Arrigoni G, Yasmin T, Carletti P. Protein Profiling of Arabidopsis Roots Treated With Humic Substances: Insights Into the Metabolic and Interactome Networks. FRONTIERS IN PLANT SCIENCE 2018; 9:1812. [PMID: 30619394 PMCID: PMC6299182 DOI: 10.3389/fpls.2018.01812] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 11/21/2018] [Indexed: 05/06/2023]
Abstract
Background and Aim: Humic substances (HSs) influence the chemical and physical properties of the soil, and are also known to affect plant physiology and nutrient uptake. This study aimed to elucidate plant metabolic pathways and physiological processes influenced by HS activity. Methods: Arabidopsis roots were treated with HS for 8 h. Quantitative mass spectrometry-based proteomics analysis of root proteins was performed using the iTRAQ (Isobaric Tag for Relative and Absolute Quantification) technique. Out of 902 protein families identified and quantified for HS treated vs. untreated roots, 92 proteins had different relative content. Bioinformatic tools such as STRING, KEGG, IIS and Cytoscape were used to interpret the biological function, pathway analysis and visualization of network amongst the identified proteins. Results: From this analysis it was possible to evaluate that all of the identified proteins were functionally classified into several categories, mainly redox homeostasis, response to inorganic substances, energy metabolism, protein synthesis, cell trafficking, and division. Conclusion: In the present study an overview of the metabolic pathways most modified by HS biological activity is provided. Activation of enzymes of the glycolytic pathway and up regulation of ribosomal protein indicated a stimulation in energy metabolism and protein synthesis. Regulation of the enzymes involved in redox homeostasis suggest a pivotal role of reactive oxygen species in the signaling and modulation of HS-induced responses.
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Affiliation(s)
- Sohaib Roomi
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Antonio Masi
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Padua, Italy
| | | | - Sara Trevisan
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Padua, Italy
| | - Silvia Quaggiotti
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Padua, Italy
| | - Micaela Pivato
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Padua, Italy
| | - Giorgio Arrigoni
- Proteomics Center, University of Padua and Azienda Ospedaliera di Padova, Padua, Italy
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Tayyaba Yasmin
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Paolo Carletti
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Padua, Italy
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18
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Heberle H, Carazzolle MF, Telles GP, Meirelles GV, Minghim R. CellNetVis: a web tool for visualization of biological networks using force-directed layout constrained by cellular components. BMC Bioinformatics 2017; 18:395. [PMID: 28929969 PMCID: PMC5606216 DOI: 10.1186/s12859-017-1787-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The advent of "omics" science has brought new perspectives in contemporary biology through the high-throughput analyses of molecular interactions, providing new clues in protein/gene function and in the organization of biological pathways. Biomolecular interaction networks, or graphs, are simple abstract representations where the components of a cell (e.g. proteins, metabolites etc.) are represented by nodes and their interactions are represented by edges. An appropriate visualization of data is crucial for understanding such networks, since pathways are related to functions that occur in specific regions of the cell. The force-directed layout is an important and widely used technique to draw networks according to their topologies. Placing the networks into cellular compartments helps to quickly identify where network elements are located and, more specifically, concentrated. Currently, only a few tools provide the capability of visually organizing networks by cellular compartments. Most of them cannot handle large and dense networks. Even for small networks with hundreds of nodes the available tools are not able to reposition the network while the user is interacting, limiting the visual exploration capability. RESULTS Here we propose CellNetVis, a web tool to easily display biological networks in a cell diagram employing a constrained force-directed layout algorithm. The tool is freely available and open-source. It was originally designed for networks generated by the Integrated Interactome System and can be used with networks from others databases, like InnateDB. CONCLUSIONS CellNetVis has demonstrated to be applicable for dynamic investigation of complex networks over a consistent representation of a cell on the Web, with capabilities not matched elsewhere.
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Affiliation(s)
- Henry Heberle
- University of São Paulo, Instituto de Ciências Matemáticas e de Computação, Av. Trabalhador São-carlense, 400, São Carlos-SP, Brazil
| | | | - Guilherme P Telles
- University of Campinas, Institute of Computing, Av. Albert Einstein, 1251, Campinas-SP, Brazil
| | | | - Rosane Minghim
- University of São Paulo, Instituto de Ciências Matemáticas e de Computação, Av. Trabalhador São-carlense, 400, São Carlos-SP, Brazil.
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19
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Saito Â, Souza EE, Costa FC, Meirelles GV, Gonçalves KA, Santos MT, Bressan GC, McComb ME, Costello CE, Whelan SA, Kobarg J. Human Regulatory Protein Ki-1/57 Is a Target of SUMOylation and Affects PML Nuclear Body Formation. J Proteome Res 2017; 16:3147-3157. [PMID: 28695742 DOI: 10.1021/acs.jproteome.7b00001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ki-1/57 is a nuclear and cytoplasmic regulatory protein first identified in malignant cells from Hodgkin's lymphoma. It is involved in gene expression regulation on both transcriptional and mRNA metabolism levels. Ki-1/57 belongs to the family of intrinsically unstructured proteins and undergoes phosphorylation by PKC and methylation by PRMT1. Previous characterization of its protein interaction profile by yeast two-hybrid screening showed that Ki-1/57 interacts with proteins of the SUMOylation machinery, the SUMO E2 conjugating enzyme UBC9 and the SUMO E3 ligase PIAS3, which suggested that Ki-1/57 could be involved with this process. Here we identified seven potential SUMO target sites (lysine residues) on Ki-1/57 sequence and observed that Ki-1/57 is modified by SUMO proteins in vitro and in vivo. We showed that SUMOylation of Ki-1/57 occurred on lysines 213, 276, and 336. In transfected cells expressing FLAG-Ki-1/57 wild-type, its paralog FLAG-CGI-55 wild-type, or their non-SUMOylated triple mutants, the number of PML-nuclear bodies (PML-NBs) is reduced compared with the control cells not expressing the constructs. More interestingly, after treating cells with arsenic trioxide (As2O3), the number of PML-NBs is no longer reduced when the non-SUMOylated triple mutant Ki-1/57 is expressed, suggesting that the SUMOylation of Ki-1/57 has a role in the control of As2O3-induced PML-NB formation. A proteome-wide analysis of Ki-1/57 partners in the presence of either SUMO-1 or SUMO-2 suggests that the involvement of Ki-1/57 with the regulation of gene expression is independent of the presence of either SUMO-1 or SUMO-2; however, the presence of SUMO-1 strongly influences the interaction of Ki-1/57 with proteins associated with cellular metabolism, maintenance, and cell cycle.
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Affiliation(s)
- Ângela Saito
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) , Campinas, São Paulo 13083-970, Brazil
| | - Edmarcia E Souza
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas , Campinas, São Paulo 13083-859, Brazil
| | - Fernanda C Costa
- Instituto de Física de São Carlos, Universidade de São Paulo , São Carlos, São Paulo 13563-120, Brazil
| | - Gabriela V Meirelles
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) , Campinas, São Paulo 13083-970, Brazil
| | - Kaliandra A Gonçalves
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) , Campinas, São Paulo 13083-970, Brazil
| | - Marcos T Santos
- ONKOS Molecular Diagnostics, Inc. , R&D Department, Ribeirão Preto, São Paulo 14056-680, Brazil
| | - Gustavo C Bressan
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa (UFV) , Viçosa, Minas Gerais 36570-000, Brazil
| | - Mark E McComb
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine , Boston, Massachusetts 02118, United States
| | - Catherine E Costello
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine , Boston, Massachusetts 02118, United States
| | - Stephen A Whelan
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine , Boston, Massachusetts 02118, United States
| | - Jörg Kobarg
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas , Campinas, São Paulo 13083-859, Brazil.,Departamento de Bioquímica e Biologia Tecidual, Programa de Pós-graduação em Biologia Funcional e Molecular, Universidade Estadual de Campinas , Campinas, São Paulo 13083-862, Brazil
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20
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NEK1 kinase domain structure and its dynamic protein interactome after exposure to Cisplatin. Sci Rep 2017; 7:5445. [PMID: 28710492 PMCID: PMC5511132 DOI: 10.1038/s41598-017-05325-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/02/2017] [Indexed: 11/11/2022] Open
Abstract
NEK family kinases are serine/threonine kinases that have been functionally implicated in the regulation of the disjunction of the centrosome, the assembly of the mitotic spindle, the function of the primary cilium and the DNA damage response. NEK1 shows pleiotropic functions and has been found to be mutated in cancer cells, ciliopathies such as the polycystic kidney disease, as well as in the genetic diseases short-rib thoracic dysplasia, Mohr-syndrome and amyotrophic lateral sclerosis. NEK1 is essential for the ionizing radiation DNA damage response and priming of the ATR kinase and of Rad54 through phosphorylation. Here we report on the structure of the kinase domain of human NEK1 in its apo- and ATP-mimetic inhibitor bound forms. The inhibitor bound structure may allow the design of NEK specific chemo-sensitizing agents to act in conjunction with chemo- or radiation therapy of cancer cells. Furthermore, we characterized the dynamic protein interactome of NEK1 after DNA damage challenge with cisplatin. Our data suggest that NEK1 and its interaction partners trigger the DNA damage pathways responsible for correcting DNA crosslinks.
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21
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Perez de Souza L, Naake T, Tohge T, Fernie AR. From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics. Gigascience 2017; 6:1-20. [PMID: 28520864 PMCID: PMC5499862 DOI: 10.1093/gigascience/gix037] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/08/2017] [Accepted: 05/12/2017] [Indexed: 01/19/2023] Open
Abstract
The grand challenge currently facing metabolomics is the expansion of the coverage of the metabolome from a minor percentage of the metabolic complement of the cell toward the level of coverage afforded by other post-genomic technologies such as transcriptomics and proteomics. In plants, this problem is exacerbated by the sheer diversity of chemicals that constitute the metabolome, with the number of metabolites in the plant kingdom generally considered to be in excess of 200 000. In this review, we focus on web resources that can be exploited in order to improve analyte and ultimately metabolite identification and quantification. There is a wide range of available software that not only aids in this but also in the related area of peak alignment; however, for the uninitiated, choosing which program to use is a daunting task. For this reason, we provide an overview of the pros and cons of the software as well as comments regarding the level of programing skills required to effectively exploit their basic functions. In addition, the torrent of available genome and transcriptome sequences that followed the advent of next-generation sequencing has opened up further valuable resources for metabolite identification. All things considered, we posit that only via a continued communal sharing of information such as that deposited in the databases described within the article are we likely to be able to make significant headway toward improving our coverage of the plant metabolome.
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Affiliation(s)
- Leonardo Perez de Souza
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Thomas Naake
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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Bernardo L, Morcia C, Carletti P, Ghizzoni R, Badeck FW, Rizza F, Lucini L, Terzi V. Proteomic insight into the mitigation of wheat root drought stress by arbuscular mycorrhizae. J Proteomics 2017; 169:21-32. [PMID: 28366879 DOI: 10.1016/j.jprot.2017.03.024] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/20/2017] [Accepted: 03/28/2017] [Indexed: 10/19/2022]
Abstract
Arbuscular mycorrhizal fungi (AMF) are plant growth promoters that ameliorate plant-water relations and the nutrient uptake of wheat. In this work, two cultivars of Triticum spp., a bread and a durum wheat, grown under drought stress and inoculated or not by AMF, are evaluated through a shotgun proteomic approach. The AMF association had beneficial effects as compared to non-mycorrhizal roots, in both bread and durum wheat. The beneficial symbiosis was confirmed by measuring morphological and physiological traits. In our work, we identified 50 statistically differential proteins in the bread wheat cultivar and 66 differential proteins in the durum wheat cultivar. The findings highlighted a modulation of proteins related to sugar metabolism, cell wall rearrangement, cytoskeletal organization and sulphur-containing proteins, as well as proteins related to plant stress responses. Among differentially expressed proteins both cultivars evidenced a decrease in sucrose:fructan 6-fructosyltransferas. In durum wheat oxylipin signalling pathway was involved with two proteins: increased 12-oxo-phytodienoic acid reductase and decreased jasmonate-induced protein, both related to the biosynthesis of jasmonic acid. Interactome analysis highlighted the possible involvement of ubiquitin although not evidenced among differentially expressed proteins. The AMF association helps wheat roots reducing the osmotic stress and maintaining cellular integrity. BIOLOGICAL SIGNIFICANCE Drought is one of the major constraints that plants must face in some areas of the world, associated to climate change, negatively affecting the worldwide plant productivity. The adoption of innovative agronomic protocols may represent a winning strategy in facing this challenge. The arbuscular mycorrhizal fungi (AMF) inoculation may represent a natural and sustainable way to mitigate the negative effects due to drought in several crop, ameliorating plant growth and development. Studies on the proteomic responses specific to AMF in drought-stressed plants will help clarify how mycorrhization elicits plant growth, nutrient uptake, and stress-tolerance responses. Such studies also offer the potential to find biological markers and genetic targets to be used during breeding for new drought-resistant varieties.
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Affiliation(s)
- Letizia Bernardo
- Genomics Research Centre (CREA-GPG), Council for Agricultural Research and Economics, Via San Protaso 302, I-29017 Fiorenzuola d'Arda, PC, Italy.
| | - Caterina Morcia
- Genomics Research Centre (CREA-GPG), Council for Agricultural Research and Economics, Via San Protaso 302, I-29017 Fiorenzuola d'Arda, PC, Italy
| | - Paolo Carletti
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Viale dell'Università, 16, I-35020 Legnaro, PD, Italy
| | - Roberta Ghizzoni
- Genomics Research Centre (CREA-GPG), Council for Agricultural Research and Economics, Via San Protaso 302, I-29017 Fiorenzuola d'Arda, PC, Italy
| | - Franz W Badeck
- Genomics Research Centre (CREA-GPG), Council for Agricultural Research and Economics, Via San Protaso 302, I-29017 Fiorenzuola d'Arda, PC, Italy
| | - Fulvia Rizza
- Genomics Research Centre (CREA-GPG), Council for Agricultural Research and Economics, Via San Protaso 302, I-29017 Fiorenzuola d'Arda, PC, Italy
| | - Luigi Lucini
- Institute of Environmental and Agricultural Chemistry, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, I-29122 PC, Italy
| | - Valeria Terzi
- Genomics Research Centre (CREA-GPG), Council for Agricultural Research and Economics, Via San Protaso 302, I-29017 Fiorenzuola d'Arda, PC, Italy
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Korvala J, Jee K, Porkola E, Almangush A, Mosakhani N, Bitu C, Cervigne NK, Zandonadi FS, Meirelles GV, Leme AFP, Coletta RD, Leivo I, Salo T. MicroRNA and protein profiles in invasive versus non-invasive oral tongue squamous cell carcinoma cells in vitro. Exp Cell Res 2017; 350:9-18. [DOI: 10.1016/j.yexcr.2016.10.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 10/10/2016] [Accepted: 10/18/2016] [Indexed: 01/08/2023]
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24
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Kawahara R, Meirelles GV, Heberle H, Domingues RR, Granato DC, Yokoo S, Canevarolo RR, Winck FV, Ribeiro ACP, Brandão TB, Filgueiras PR, Cruz KSP, Barbuto JA, Poppi RJ, Minghim R, Telles GP, Fonseca FP, Fox JW, Santos-Silva AR, Coletta RD, Sherman NE, Paes Leme AF. Integrative analysis to select cancer candidate biomarkers to targeted validation. Oncotarget 2016; 6:43635-52. [PMID: 26540631 PMCID: PMC4791256 DOI: 10.18632/oncotarget.6018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 10/17/2015] [Indexed: 01/15/2023] Open
Abstract
Targeted proteomics has flourished as the method of choice for prospecting for and validating potential candidate biomarkers in many diseases. However, challenges still remain due to the lack of standardized routines that can prioritize a limited number of proteins to be further validated in human samples. To help researchers identify candidate biomarkers that best characterize their samples under study, a well-designed integrative analysis pipeline, comprising MS-based discovery, feature selection methods, clustering techniques, bioinformatic analyses and targeted approaches was performed using discovery-based proteomic data from the secretomes of three classes of human cell lines (carcinoma, melanoma and non-cancerous). Three feature selection algorithms, namely, Beta-binomial, Nearest Shrunken Centroids (NSC), and Support Vector Machine-Recursive Features Elimination (SVM-RFE), indicated a panel of 137 candidate biomarkers for carcinoma and 271 for melanoma, which were differentially abundant between the tumor classes. We further tested the strength of the pipeline in selecting candidate biomarkers by immunoblotting, human tissue microarrays, label-free targeted MS and functional experiments. In conclusion, the proposed integrative analysis was able to pre-qualify and prioritize candidate biomarkers from discovery-based proteomics to targeted MS.
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Affiliation(s)
- Rebeca Kawahara
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Gabriela V Meirelles
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Henry Heberle
- Instituto de Ciências Matemáticas e de Computação, Universidade de São Paulo, USP, São Carlos, Brazil
| | - Romênia R Domingues
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Daniela C Granato
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Sami Yokoo
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Rafael R Canevarolo
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil.,Centro Infantil Boldrini, Campinas, Brazil
| | - Flavia V Winck
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Ana Carolina P Ribeiro
- Instituto do Câncer do Estado de São Paulo, Octavio Frias de Oliveira, São Paulo, Brazil
| | - Thaís Bianca Brandão
- Instituto do Câncer do Estado de São Paulo, Octavio Frias de Oliveira, São Paulo, Brazil
| | - Paulo R Filgueiras
- Instituto de Química, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil
| | - Karen S P Cruz
- Instituto de Ciências Biomédicas, Departamento de Imunologia, Universidade de São Paulo, USP, São Paulo, Brazil
| | - José Alexandre Barbuto
- Instituto de Ciências Biomédicas, Departamento de Imunologia, Universidade de São Paulo, USP, São Paulo, Brazil
| | - Ronei J Poppi
- Instituto de Química, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil
| | - Rosane Minghim
- Instituto de Ciências Matemáticas e de Computação, Universidade de São Paulo, USP, São Carlos, Brazil
| | - Guilherme P Telles
- Instituto de Computação, Universidade Estadual de Campinas, UNICAMP, Campinas, Brazil
| | - Felipe Paiva Fonseca
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil
| | - Jay W Fox
- W. M. Keck Biomedical Mass Spectrometry Lab, University of Virginia, Charlottesville, Virginia, USA
| | - Alan R Santos-Silva
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil
| | - Ricardo D Coletta
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil
| | - Nicholas E Sherman
- W. M. Keck Biomedical Mass Spectrometry Lab, University of Virginia, Charlottesville, Virginia, USA
| | - Adriana F Paes Leme
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
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Pavan ICB, Yokoo S, Granato DC, Meneguello L, Carnielli CM, Tavares MR, do Amaral CL, de Freitas LB, Paes Leme AF, Luchessi AD, Simabuco FM. Different interactomes for p70-S6K1 and p54-S6K2 revealed by proteomic analysis. Proteomics 2016; 16:2650-2666. [PMID: 27493124 DOI: 10.1002/pmic.201500249] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 06/28/2016] [Accepted: 08/03/2016] [Indexed: 01/04/2023]
Abstract
S6Ks are major effectors of the mTOR (mammalian target of rapamycin) pathway, signaling for increased protein synthesis and cell growth in response to insulin, AMP/ATP levels, and amino acids. Deregulation of this pathway has been related to disorders and diseases associated with metabolism, such as obesity, diabetes, and cancer. S6K family is composed of two main members, S6K1 and S6K2, which comprise different isoforms resulted from alternative splicing or alternative start codon use. Although important molecular functions have been associated with p70-S6K1, the most extensively studied isoform, the S6K2 counterpart lacks information. In the present study, we performed immunoprecipitation assays followed by mass spectrometry (MS) analysis of FLAG-tagged p70-S6K1 and p54-S6K2 interactomes, after expression in HEK293 cells. Protein lists were submitted to CRAPome (Contaminant Repository for Affinity Purification) and SAINT (Significance Analysis of INTeractome) analysis, which allowed the identification of high-scoring interactions. By a comparative approach, p70-S6K1 interacting proteins were predominantly related to "cytoskeleton" and "stress response," whereas p54-S6K2 interactome was more associated to "transcription," "splicing," and "ribosome biogenesis." Moreover, we have found evidences for new targets or regulators of the S6K protein family, such as proteins NCL, NPM1, eIF2α, XRCC6, PARP1, and ILF2/ILF3 complex. This study provides new information about the interacting networks of S6Ks, which may contribute for future approaches to a better understanding of the mTOR/S6K pathway.
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Affiliation(s)
- Isadora C B Pavan
- Laboratory of Metabolic Disorders, School of Applied Sciences, University of Campinas, Limeira, São Paulo, Brazil
| | - Sami Yokoo
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Daniela C Granato
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Letícia Meneguello
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas, Limeira, São Paulo, Brazil
| | - Carolina M Carnielli
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Mariana R Tavares
- Laboratory of Metabolic Disorders, School of Applied Sciences, University of Campinas, Limeira, São Paulo, Brazil
| | - Camila L do Amaral
- Laboratory of Metabolic Disorders, School of Applied Sciences, University of Campinas, Limeira, São Paulo, Brazil
| | - Lidia B de Freitas
- Laboratory of Metabolic Disorders, School of Applied Sciences, University of Campinas, Limeira, São Paulo, Brazil
| | - Adriana F Paes Leme
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Augusto D Luchessi
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas, Limeira, São Paulo, Brazil
| | - Fernando M Simabuco
- Laboratory of Metabolic Disorders, School of Applied Sciences, University of Campinas, Limeira, São Paulo, Brazil.
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Carnielli CM, Artier J, Franco de Oliveira JC, Novo-Mansur MTM. Interaction network and mass spectrometry data of Xanthomonas citri subsp. citri surface proteins from differential proteomic analysis of infectious and non-infectious cells. Data Brief 2016; 8:1400-11. [PMID: 27595129 PMCID: PMC4995475 DOI: 10.1016/j.dib.2016.07.054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/24/2016] [Accepted: 07/26/2016] [Indexed: 12/04/2022] Open
Abstract
Here we provide the mass-spectrometry and in silico interaction network dataset of proteins identified on our research article on surface proteomic analysis from Xanthomonas citri subsp. citri (XAC) cells grown in vivo (infectious) and in vitro (non-infectious, control) by 2D-DIGE approach. Fluorescence labeling of proteins were performed on intact cells followed by cellular lysis and labeled spots from 2D gel differing in abundance between the two conditions (ANOVA, p-value<0.05) were analyzed by a nano-electrospray tandem mass spectrometry Q-Tof Ultima API mass spectrometer (MicroMass/Waters) (LC-ESI-MS/MS). This article contains raw data of proteins detected in the 79 spots analyzed by LC-ESI-MS/MS approach and also an enrichment analysis on the resulting protein–protein interaction network performed with the Integrated Interactome System (IIS) platform and Cytoscape software. The data are supplementary to our original research article, “Xanthomonas citri subsp. citri surface proteome by 2D-DIGE: ferric enterobactin receptor and other outer membrane proteins potentially involved in citric host interaction” (Carnielli et al., 2016) [1], and raw data are available via Peptide Atlas (ftp://PASS00850:ZJ7425v@ftp.peptideatlas.org/).
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Affiliation(s)
- Carolina Moretto Carnielli
- Laboratório de Bioquímica e Biologia Molecular Aplicada- LBBMA, Departamento de Genética e Evolução, Universidade Federal de São Carlos, UFSCar, São Carlos, SP, Brazil
| | - Juliana Artier
- Laboratório de Bioquímica e Biologia Molecular Aplicada- LBBMA, Departamento de Genética e Evolução, Universidade Federal de São Carlos, UFSCar, São Carlos, SP, Brazil
| | - Julio Cezar Franco de Oliveira
- Laboratório de Interações Microbianas, Departamento de Ciências Biológicas, Universidade Federal de São Paulo, UNIFESP, Diadema, SP, Brazil
| | - Maria Teresa Marques Novo-Mansur
- Laboratório de Bioquímica e Biologia Molecular Aplicada- LBBMA, Departamento de Genética e Evolução, Universidade Federal de São Carlos, UFSCar, São Carlos, SP, Brazil
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Delmonico L, Bravo M, Silvestre RT, Ornellas MHF, De Azevedo CM, Alves G. Proteomic profile of saliva and plasma from women with impalpable breast lesions. Oncol Lett 2016; 12:2145-2152. [PMID: 27602154 PMCID: PMC4998569 DOI: 10.3892/ol.2016.4828] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 06/10/2016] [Indexed: 12/22/2022] Open
Abstract
The present study evaluated the proteomic profile of saliva and plasma from women with impalpable breast lesions using nano-liquid chromatography-quadrupole-time-of-flight (nLC-Q-TOF) technology. Plasma and saliva from patients with fibroadenoma (n=10), infiltrating ductal carcinoma (n=10) and healthy control groups (n=8) were assessed by combinations of inter/intra-group analyses, revealing significant quantitative and qualitative differences. The major differentially-expressed proteins in the saliva of patients compared with the controls were α2-macroglobulin and ceruloplasmin, but the proteins that met the minimum fold-change and P-value cut-offs were leukocyte elastase inhibitor and α-enolase, and deleted in malignant brain tumors 1. Concerning plasma, α-2-macroglobulin and ceruplasmin were upregulated, while other proteins such as haptoglobin, hemopexin and vitamin D-binding protein were downregulated compared with the control. The changes in immune, molecular transport and signaling pathways were the most representative in the proteomic profile of the saliva and plasma. This is the first study to describe the proteome of saliva and plasma from the same women with impalpable breast lesions.
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Affiliation(s)
- Lucas Delmonico
- Research Coordination, National Cancer Institute, Rio de Janeiro 20230-130, Brazil
- Graduate Program of Medical Sciences, State University of Rio de Janeiro, Rio de Janeiro 20550-170, Brazil
- Circulating Markers Laboratory, Faculty of Medical Sciences, State University of Rio de Janeiro, Rio de Janeiro 20550-170, Brazil
| | - Maryah Bravo
- Research Coordination, National Cancer Institute, Rio de Janeiro 20230-130, Brazil
- Circulating Markers Laboratory, Faculty of Medical Sciences, State University of Rio de Janeiro, Rio de Janeiro 20550-170, Brazil
| | - Rafaele Tavares Silvestre
- Research Coordination, National Cancer Institute, Rio de Janeiro 20230-130, Brazil
- Graduate Program of Medical Sciences, State University of Rio de Janeiro, Rio de Janeiro 20550-170, Brazil
- Circulating Markers Laboratory, Faculty of Medical Sciences, State University of Rio de Janeiro, Rio de Janeiro 20550-170, Brazil
| | - Maria Helena Faria Ornellas
- Graduate Program of Medical Sciences, State University of Rio de Janeiro, Rio de Janeiro 20550-170, Brazil
- Circulating Markers Laboratory, Faculty of Medical Sciences, State University of Rio de Janeiro, Rio de Janeiro 20550-170, Brazil
| | | | - Gilda Alves
- Research Coordination, National Cancer Institute, Rio de Janeiro 20230-130, Brazil
- Graduate Program of Medical Sciences, State University of Rio de Janeiro, Rio de Janeiro 20550-170, Brazil
- Circulating Markers Laboratory, Faculty of Medical Sciences, State University of Rio de Janeiro, Rio de Janeiro 20550-170, Brazil
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de Souza EE, Hehnly H, Perez AM, Meirelles GV, Smetana JHC, Doxsey S, Kobarg J. Human Nek7-interactor RGS2 is required for mitotic spindle organization. Cell Cycle 2015; 14:656-67. [PMID: 25664600 DOI: 10.4161/15384101.2014.994988] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The mitotic spindle apparatus is composed of microtubule (MT) networks attached to kinetochores organized from 2 centrosomes (a.k.a. spindle poles). In addition to this central spindle apparatus, astral MTs assemble at the mitotic spindle pole and attach to the cell cortex to ensure appropriate spindle orientation. We propose that cell cycle-related kinase, Nek7, and its novel interacting protein RGS2, are involved in mitosis regulation and spindle formation. We found that RGS2 localizes to the mitotic spindle in a Nek7-dependent manner, and along with Nek7 contributes to spindle morphology and mitotic spindle pole integrity. RGS2-depletion leads to a mitotic-delay and severe defects in the chromosomes alignment and congression. Importantly, RGS2 or Nek7 depletion or even overexpression of wild-type or kinase-dead Nek7, reduced γ-tubulin from the mitotic spindle poles. In addition to causing a mitotic delay, RGS2 depletion induced mitotic spindle misorientation coinciding with astral MT-reduction. We propose that these phenotypes directly contribute to a failure in mitotic spindle alignment to the substratum. In conclusion, we suggest a molecular mechanism whereupon Nek7 and RGS2 may act cooperatively to ensure proper mitotic spindle organization.
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Key Words
- CREST, calcium-responsive transactivator
- EB1, end-binding protein 1
- GAP, GTPase-activating protein
- MT, microtubule
- Nek, NIMA-related kinase
- Nek7
- PCM, centrosomal pericentriolar material
- PD, pull-down
- PPI, protein-protein interaction
- RGS, regulators of G protein signaling
- RGS2
- WB, Western blotting
- cell division
- mitotic spindle
- mitotic spindle orientation
- shRNA, short-interfering RNA
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Affiliation(s)
- Edmarcia Elisa de Souza
- a Laboratório Nacional de Biociências-LNBio ; Centro Nacional de Pesquisa em Energia e Materiais-CNPEM ; Campinas , SP Brasil
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Misra BB, van der Hooft JJJ. Updates in metabolomics tools and resources: 2014-2015. Electrophoresis 2015; 37:86-110. [DOI: 10.1002/elps.201500417] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 10/04/2015] [Accepted: 10/05/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Biswapriya B. Misra
- Department of Biology, Genetics Institute; University of Florida; Gainesville FL USA
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Peloso EF, Dias L, Queiroz RML, Leme AFPP, Pereira CN, Carnielli CM, Werneck CC, Sousa MV, Ricart CAO, Gadelha FR. Trypanosoma cruzi mitochondrial tryparedoxin peroxidase is located throughout the cell and its pull down provides one step towards the understanding of its mechanism of action. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:1-10. [PMID: 26527457 DOI: 10.1016/j.bbapap.2015.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/23/2015] [Accepted: 10/16/2015] [Indexed: 01/11/2023]
Abstract
Trypanosoma cruzi depends on the effectiveness of redox metabolism to survive and ensure infection in the host. Homeostasis of redox metabolism in T. cruzi is achieved by the actions of several proteins that differ in many aspects from host proteins. Although extensive research has been performed examining hydroperoxide cytosolic antioxidant defense centered on trypanothione, the mechanisms of mitochondrial antioxidant defense are not yet known. The aim of this study was to elucidate the partners of TcMPx antioxidant pathway and to determine the influence of the cellular context (physiological versus oxidative stress). Through co-precipitation coupled with a mass spectrometry approach, a variety of proteins were detected under physiological and oxidative stress conditions. Interestingly, functional category analysis of the proteins identified under physiological conditions showed that they were involved in the stress response, oxidoreduction, thiol transfer, and metabolic processes; this profile is distinct under oxidative stress conditions likely due to structural alterations. Our findings help to elucidate the reactions involving TcMPx and most importantly also reveal that this protein is present throughout the cell and that its interaction partners change following oxidative stress exposure. The involvement and significance of the proteins found to interact with TcMPx and other possible functions for this protein are discussed widening our knowledge regarding T. cruzi mitochondrial antioxidant defenses.
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Affiliation(s)
- E F Peloso
- Departamento de Bioquímica e Biologia Tecidual, UNICAMP, Campinas, SP, Brazil
| | - L Dias
- Departamento de Bioquímica e Biologia Tecidual, UNICAMP, Campinas, SP, Brazil
| | - R M L Queiroz
- Laboratório de Bioquímica e Química de Proteínas, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - A F P Paes Leme
- Centro Nacional de Pesquisa em Energia e Materiais, Laboratório Nacional de Biociências, Campinas, SP, Brazil
| | - C N Pereira
- Departamento de Bioquímica e Biologia Tecidual, UNICAMP, Campinas, SP, Brazil
| | - C M Carnielli
- Centro Nacional de Pesquisa em Energia e Materiais, Laboratório Nacional de Biociências, Campinas, SP, Brazil
| | - C C Werneck
- Departamento de Bioquímica e Biologia Tecidual, UNICAMP, Campinas, SP, Brazil
| | - M V Sousa
- Laboratório de Bioquímica e Química de Proteínas, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - C A O Ricart
- Laboratório de Bioquímica e Química de Proteínas, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - F R Gadelha
- Departamento de Bioquímica e Biologia Tecidual, UNICAMP, Campinas, SP, Brazil.
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Basei FL, Meirelles GV, Righetto GL, Dos Santos Migueleti DL, Smetana JHC, Kobarg J. New interaction partners for Nek4.1 and Nek4.2 isoforms: from the DNA damage response to RNA splicing. Proteome Sci 2015; 13:11. [PMID: 25798074 PMCID: PMC4367857 DOI: 10.1186/s12953-015-0065-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 02/09/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Neks are serine-threonine kinases that are similar to NIMA, a protein found in Aspergillus nidulans which is essential for cell division. In humans there are eleven Neks which are involved in different biological functions besides the cell cycle control. Nek4 is one of the largest members of the Nek family and has been related to the primary cilia formation and in DNA damage response. However, its substrates and interaction partners are still unknown. In an attempt to better understand the role of Nek4, we performed an interactomics study to find new biological processes in which Nek4 is involved. We also described a novel Nek4 isoform which lacks a region of 46 amino acids derived from an insertion of an Alu sequence and showed the interactomics profile of these two Nek4 proteins. RESULTS AND DISCUSSION Isoform 1 and isoform 2 of Nek4 were expressed in human cells and after an immunoprecipitation followed by mass spectrometry, 474 interacting proteins were identified for isoform 1 and 149 for isoform 2 of Nek4. About 68% of isoform 2 potential interactors (102 proteins) are common between the two Nek4 isoforms. Our results reinforce Nek4 involvement in the DNA damage response, cilia maintenance and microtubule stabilization, and raise the possibility of new functional contexts, including apoptosis signaling, stress response, translation, protein quality control and, most intriguingly, RNA splicing. We show for the first time an unexpected difference between both Nek4 isoforms in RNA splicing control. Among the interacting partners, we found important proteins such as ANT3, Whirlin, PCNA, 14-3-3ε, SRSF1, SRSF2, SRPK1 and hNRNPs proteins. CONCLUSIONS This study provides new insights into Nek4 functions, identifying new interaction partners and further suggests an interesting difference between isoform 1 and isoform 2 of this kinase. Nek4 isoform 1 may have similar roles compared to other Neks and these roles are not all preserved in isoform 2. Besides, in some processes, both isoforms showed opposite effects, indicating a possible fine controlled regulation.
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Affiliation(s)
- Fernanda Luisa Basei
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Rua Giuseppe Máximo Scolfaro 10.000, C.P.6192, 13084-971 Campinas, São Paulo Brazil ; Programa de Pós-graduação em Biologia Funcional e Molecular, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo Brazil
| | - Gabriela Vaz Meirelles
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Rua Giuseppe Máximo Scolfaro 10.000, C.P.6192, 13084-971 Campinas, São Paulo Brazil
| | - Germanna Lima Righetto
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Rua Giuseppe Máximo Scolfaro 10.000, C.P.6192, 13084-971 Campinas, São Paulo Brazil
| | - Deivid Lucas Dos Santos Migueleti
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Rua Giuseppe Máximo Scolfaro 10.000, C.P.6192, 13084-971 Campinas, São Paulo Brazil ; Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo Brazil
| | - Juliana Helena Costa Smetana
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Rua Giuseppe Máximo Scolfaro 10.000, C.P.6192, 13084-971 Campinas, São Paulo Brazil
| | - Jörg Kobarg
- Programa de Pós-graduação em Biologia Funcional e Molecular, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo Brazil ; Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo Brazil ; Instituto de Biologia, Departamento de Bioquímica e de Biologia Tecidual, Universidade Estadual de Campinas, Campinas, SP Brazil ; Universidade Estadual de Campinas, Faculdade de Ciências Farmacêuticas, Campinas, São Paulo Brazil
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Nek5 interacts with mitochondrial proteins and interferes negatively in mitochondrial mediated cell death and respiration. Cell Signal 2015; 27:1168-77. [PMID: 25725288 DOI: 10.1016/j.cellsig.2015.02.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/05/2015] [Accepted: 02/21/2015] [Indexed: 12/14/2022]
Abstract
Mitochondria are involved in energy supply, signaling, cell death and cellular differentiation and have been implicated in several human diseases. Neks (NIMA-related kinases) represent a family of mammal protein kinases that play essential roles in cell-cycle progression, but other functions have recently been related. A yeast two-hybrid (Y2H) screen was performed to identify and characterize Nek5 interaction partners and the mitochondrial proteins Cox11, MTX-2 and BCLAF1 were retrieved. Apoptosis assay showed protective effects of stable hNek5 expression from Hek293-T's cell death after thapsigargin treatment (2 μM). Nek5 silenced cells as well as cells expressing a "kinase dead" version of Nek5, displayed an increase in ROS formation after 4 h of thapsigargin treatment. Mitochondrial respiratory chain activity was found decreased upon stable hNek5expression. Cells silenced for hNek5 on the other hand presented 1.7 fold increased basal rates of respiration, especially at the electrons transfer steps from TMPD to cytochrome c and at the complex II. In conclusion, our data suggest for the first time mitochondrial localization and functions for Nek5 and its participation in cell death and cell respiration regulation. Stable expression of hNek5 in Hek293T cells resulted in enhanced cell viability, decreased cell death and drug resistance, while depletion of hNek5by shRNA overcame cancer cell drug resistance and induced apoptosis in vitro. Stable expression of hNek5 also inhibits thapsigargin promoted apoptosis and the respiratory chain complex IV in HEK293T cells.
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Carnielli CM, Winck FV, Paes Leme AF. Functional annotation and biological interpretation of proteomics data. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:46-54. [DOI: 10.1016/j.bbapap.2014.10.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 10/07/2014] [Accepted: 10/21/2014] [Indexed: 12/22/2022]
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Costa FC, Saito A, Gonçalves KA, Vidigal PM, Meirelles GV, Bressan GC, Kobarg J. Ki-1/57 and CGI-55 ectopic expression impact cellular pathways involved in proliferation and stress response regulation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:2944-56. [PMID: 25205453 DOI: 10.1016/j.bbamcr.2014.08.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 08/27/2014] [Accepted: 08/28/2014] [Indexed: 10/24/2022]
Abstract
Ki-1/57 (HABP4) and CGI-55 (SERBP1) are regulatory proteins and paralogs with 40.7% amino acid sequence identity and 67.4% similarity. Functionally, they have been implicated in the regulation of gene expression on both the transcriptional and mRNA metabolism levels. A link with tumorigenesis is suggested, since both paralogs show altered expression levels in tumor cells and the Ki-1/57 gene is found in a region of chromosome 9q that represents a haplotype for familiar colon cancer. However, the target genes regulated by Ki-1/57 and CGI-55 are unknown. Here, we analyzed the alterations of the global transcriptome profile after Ki-1/57 or CGI-55 overexpression in HEK293T cells by DNA microchip technology. We were able to identify 363 or 190 down-regulated and 50 or 27 up-regulated genes for Ki-1/57 and CGI-55, respectively, of which 20 were shared between both proteins. Expression levels of selected genes were confirmed by qRT-PCR both after protein overexpression and siRNA knockdown. The majority of the genes with altered expression were associated to proliferation, apoptosis and cell cycle control processes, prompting us to further explore these contexts experimentally. We observed that overexpression of Ki-1/57 or CGI-55 results in reduced cell proliferation, mainly due to a G1 phase arrest, whereas siRNA knockdown of CGI-55 caused an increase in proliferation. In the case of Ki-1/57 overexpression, we found protection from apoptosis after treatment with the ER-stress inducer thapsigargin. Together, our data give important new insights that may help to explain these proteins putative involvement in tumorigenic events.
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Affiliation(s)
- Fernanda C Costa
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brasil.
| | - Angela Saito
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brasil; Departamento de Bioquímica-Programa de Pós-graduação em Biologia Funcional e Molecular, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil.
| | - Kaliandra A Gonçalves
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brasil; Departamento de Bioquímica-Programa de Pós-graduação em Biologia Funcional e Molecular, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil.
| | - Pedro M Vidigal
- Laboratório de Bioinformática, Instituto de Biotecnologia Aplicada à Agropecuária-BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brasil.
| | - Gabriela V Meirelles
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brasil.
| | - Gustavo C Bressan
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brasil; Departamento de Bioquímica-Programa de Pós-graduação em Biologia Funcional e Molecular, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil.
| | - Jörg Kobarg
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brasil; Departamento de Bioquímica-Programa de Pós-graduação em Biologia Funcional e Molecular, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil; Departamento de Genética, Evolução e Bioagentes - Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil.
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de Souza EE, Meirelles GV, Godoy BB, Perez AM, Smetana JHC, Doxsey SJ, McComb ME, Costello CE, Whelan SA, Kobarg J. Characterization of the human NEK7 interactome suggests catalytic and regulatory properties distinct from those of NEK6. J Proteome Res 2014; 13:4074-90. [PMID: 25093993 PMCID: PMC4156247 DOI: 10.1021/pr500437x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human NEK7 is a regulator of cell division and plays an important role in growth and survival of mammalian cells. Human NEK6 and NEK7 are closely related, consisting of a conserved C-terminal catalytic domain and a nonconserved and disordered N-terminal regulatory domain, crucial to mediate the interactions with their respective proteins. Here, in order to better understand NEK7 cellular functions, we characterize the NEK7 interactome by two screening approaches: one using a yeast two-hybrid system and the other based on immunoprecipitation followed by mass spectrometry analysis. These approaches led to the identification of 61 NEK7 interactors that contribute to a variety of biological processes, including cell division. Combining additional interaction and phosphorylation assays from yeast two-hybrid screens, we validated CC2D1A, TUBB2B, MNAT1, and NEK9 proteins as potential NEK7 interactors and substrates. Notably, endogenous RGS2, TUBB, MNAT1, NEK9, and PLEKHA8 localized with NEK7 at key sites throughout the cell cycle, especially during mitosis and cytokinesis. Furthermore, we obtained evidence that the closely related kinases NEK6 and NEK7 do not share common interactors, with the exception of NEK9, and display different modes of protein interaction, depending on their N- and C-terminal regions, in distinct fashions. In summary, our work shows for the first time a comprehensive NEK7 interactome that, combined with functional in vitro and in vivo assays, suggests that NEK7 is a multifunctional kinase acting in different cellular processes in concert with cell division signaling and independently of NEK6.
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Affiliation(s)
- Edmarcia Elisa de Souza
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais , Campinas, São Paulo, Brazil
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