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Gazzinelli-Guimaraes PH, Bennuru S, de Queiroz Prado R, Ricciardi A, Sciurba J, Kupritz J, Moser M, Kamenyeva O, Nutman TB. House dust mite sensitization drives cross-reactive immune responses to homologous helminth proteins. PLoS Pathog 2021; 17:e1009337. [PMID: 33651853 PMCID: PMC7924806 DOI: 10.1371/journal.ppat.1009337] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 01/25/2021] [Indexed: 02/06/2023] Open
Abstract
The establishment of type 2 responses driven by allergic sensitization prior to exposure to helminth parasites has demonstrated how tissue-specific responses can protect against migrating larval stages, but, as a consequence, allow for immune-mediated, parasite/allergy-associated morbidity. In this way, whether helminth cross-reacting allergen-specific antibodies are produced and play a role during the helminth infection, or exacerbate the allergic outcome awaits elucidation. Thus, the main objective of the study was to investigate whether house dust mite (HDM) sensitization triggers allergen-specific antibodies that interact with Ascaris antigens and mediate antibody-dependent deleterious effects on these parasites as well as, to assess the capacity of cross-reactive helminth proteins to trigger allergic inflammation in house dust mite presensitized mice. Here, we show that the sensitization with HDM-extract drives marked IgE and IgG1 antibody responses that cross-react with Ascaris larval antigens. Proteomic analysis of Ascaris larval antigens recognized by these HDM-specific antibodies identified Ascaris tropomyosin and enolase as the 2 major HDM homologues based on high sequence and structural similarity. Moreover, the helminth tropomyosin could drive Type-2 associated pulmonary inflammation similar to HDM following HDM tropomyosin sensitization. The HDM-triggered IgE cross-reactive antibodies were found to be functional as they mediated immediate hypersensitivity responses in skin testing. Finally, we demonstrated that HDM sensitization in either B cells or FcγRIII alpha-chain deficient mice indicated that the allergen driven cell-mediated larval killing is not antibody-dependent. Taken together, our data suggest that aeroallergen sensitization drives helminth reactive antibodies through molecular and structural similarity between HDM and Ascaris antigens suggesting that cross-reactive immune responses help drive allergic inflammation. Epidemiological studies related to the interaction between allergies and helminth infection led to the observations that helped shape the so-called hygiene hypothesis, which generally states that chronic exposure to helminths diminishes the risk of the development of allergic disease. However, there are conflicting studies that have called this particular hypothesis into question, such as, the studies that suggest that infection with the helminth Ascaris lumbricoides is a risk factor for wheezing and atopy or can aggravate the clinical symptoms of asthma. A hypothetical explanation for such phenomenon is the fact that there is a high degree of molecular and structural similarities among helminth antigens with many common allergens, including the house dust mite (HDM). This high degree of homology of certain epitopes shared between helminths and allergens generate cross-react antibodies which may play a role in the pathogenesis or regulation of both conditions. Thus, this study aimed to understand the structural basis for cross-reactive antibodies induced by HDM sensitization. Here, we demonstrate that HDM sensitization drives helminth cross-reactive antibodies through molecular and structural homology between tropomyosins and enolases. This study highlights the pro-allergenic properties of HDM and helminth proteins that share homologous epitopes.
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Affiliation(s)
| | - Sasisekhar Bennuru
- Laboratory of Parasitic Diseases, NIAID, National Institutes of Health; Bethesda, Maryland, United States of America
| | - Rafael de Queiroz Prado
- Laboratory of Parasitic Diseases, NIAID, National Institutes of Health; Bethesda, Maryland, United States of America
| | - Alessandra Ricciardi
- Laboratory of Parasitic Diseases, NIAID, National Institutes of Health; Bethesda, Maryland, United States of America
| | - Joshua Sciurba
- Laboratory of Parasitic Diseases, NIAID, National Institutes of Health; Bethesda, Maryland, United States of America
| | - Jonah Kupritz
- Laboratory of Parasitic Diseases, NIAID, National Institutes of Health; Bethesda, Maryland, United States of America
| | - Matthew Moser
- Laboratory of Parasitic Diseases, NIAID, National Institutes of Health; Bethesda, Maryland, United States of America
| | - Olena Kamenyeva
- Biological Imaging Section of Research Technologies Branch, National Institutes of Health; Bethesda, Maryland, United States of America
| | - Thomas B. Nutman
- Laboratory of Parasitic Diseases, NIAID, National Institutes of Health; Bethesda, Maryland, United States of America
- * E-mail: (PHGG); (TBN)
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Deolankar SC, Modi PK, Subbannayya Y, Pervaje R, Prasad TSK. Molecular Targets from Traditional Medicines for Neuroprotection in Human Neurodegenerative Diseases. ACTA ACUST UNITED AC 2020; 24:394-403. [DOI: 10.1089/omi.2020.0033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sayali Chandrashekhar Deolankar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Prashant Kumar Modi
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Yashwanth Subbannayya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
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Rybarczyk J, Khalenkow D, Kieckens E, Skirtach AG, Cox E, Vanrompay D. Lactoferrin translocates to the nucleus of bovine rectal epithelial cells in the presence of Escherichia coli O157:H7. Vet Res 2019; 50:75. [PMID: 31570109 PMCID: PMC6771091 DOI: 10.1186/s13567-019-0694-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/22/2019] [Indexed: 01/12/2023] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is a foodborne pathogen which causes illness in humans. Ruminants are the main reservoirs and EHEC predominantly colonizes the epithelium of the recto-anal junction of cattle. Immunosuppression by EHEC promotes re-infection of cattle. However, bovine lactoferrin (bLF) apparently can overrule the immunosuppression by inducing EHEC-specific IgA responses at the mucosal site. The IgA responses are significantly correlated with reduced EHEC shedding and the absence of colonization at the rectal mucosa following re-infection. Therefore, to examine the interaction between bLF and bovine rectal epithelial cells, we first developed a method to establish a primary cell culture of epithelial cells of the rectum of cattle. Furthermore, we used LC–MS/MS to demonstrate the presence of secreted lactoferrin in bovine milk and the absence of a “delta” isoform which is known to translocate to the nucleus of cells. Nevertheless, lactoferrin derived from bovine milk was internalized by rectal epithelial cells and translocated to the nuclei. Moreover, nuclear translocation of bLF was significantly enhanced when the epithelial cells were inoculated with EHEC, as demonstrated by confocal fluorescence microscopy and confirmed by Raman microscopy and 3D imaging.
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Affiliation(s)
- Joanna Rybarczyk
- Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium.
| | - Dmitry Khalenkow
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium
| | - Evelien Kieckens
- Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium
| | - Andre G Skirtach
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium
| | - Eric Cox
- Laboratory of Immunology, Faculty of Veterinary Medicine, Ghent University, 9000, Ghent, Belgium
| | - Daisy Vanrompay
- Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium
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Abstract
Mass spectrometry (MS) is the core for advanced methods in proteomic experiments. When effectively used, proteomics may provide extensive information about proteins and their post-translational modifications, as well as their interaction partners. However, there are also many problems that one can encounter during a proteomic experiment, including, but not limited to sample preparation, sample fractionation, sample analysis, data analysis & interpretation and biological significance. Here we discuss some of the problems that researchers should be aware of when performing a proteomic experiment.
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Affiliation(s)
- Devika Channaveerappa
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Armand G Ngounou Wetie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Costel C Darie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA.
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Aslebagh R, Wormwood KL, Channaveerappa D, Wetie AGN, Woods AG, Darie CC. Identification of Posttranslational Modifications (PTMs) of Proteins by Mass Spectrometry. Advances in Experimental Medicine and Biology 2019; 1140:199-224. [DOI: 10.1007/978-3-030-15950-4_11] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Ngounou Wetie AG, Sokolowska I, Channaveerappa D, Dupree EJ, Jayathirtha M, Woods AG, Darie CC. Proteomics and Non-proteomics Approaches to Study Stable and Transient Protein-Protein Interactions. Advances in Experimental Medicine and Biology 2019; 1140:121-142. [DOI: 10.1007/978-3-030-15950-4_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Sokolowska I, Ngounou Wetie AG, Woods AG, Jayathirtha M, Darie CC. Role of Mass Spectrometry in Investigating a Novel Protein: The Example of Tumor Differentiation Factor (TDF). Adv Exp Med Biol 2019; 1140:417-433. [PMID: 31347062 DOI: 10.1007/978-3-030-15950-4_24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Better understanding of central nervous system (CNS) molecules can include the identification of new molecules and their receptor systems. Discovery of novel proteins and elucidation of receptor targets can be accomplished using mass spectrometry (MS). We describe a case study of such a molecule, which our lab has studied using MS in combination with other protein identification techniques, such as immunohistochemistry and Western Blotting. This molecule is known as tumor differentiation factor (TDF), a recently-found protein secreted by the pituitary into the blood. TDF mRNA has been detected in brain; not heart, placenta, lung, liver, skeletal muscle, or pancreas. Currently TDF has an unclear function, and prior to our studies, its localization was only minimally understood, with no understanding of receptor targets. We investigated the distribution of TDF in the rat brain using immunohistochemistry (IHC) and immunofluorescence (IF). TDF protein was detected in pituitary and most other brain regions, in specific neurons but not astrocytes. We found TDF immunoreactivity in cultured neuroblastoma, not astrocytoma. These data suggest that TDF is localized to neurons, not to astrocytes. Our group also conducted studies to identify the TDF receptor (TDF-R). Using LC-MS/MS and Western blotting, we identified the members of the Heat Shock 70-kDa family of proteins (HSP70) as potential TDF-R candidates in both MCF7 and BT-549 human breast cancer cells (HBCC) and PC3, DU145, and LNCaP human prostate cancer cells (HPCC), but not in HeLa cells, NG108 neuroblastoma, or HDF-a and BLK CL.4 cells fibroblasts or fibroblast-like cells. These studies have combined directed protein identification techniques with mass spectrometry to increase our understanding of a novel protein that may have distinct actions as a hormone in the body and as a growth factor in the brain.
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Affiliation(s)
- Izabela Sokolowska
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY, USA.
| | - Armand G Ngounou Wetie
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Alisa G Woods
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Madhuri Jayathirtha
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY, USA
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Woods AG, Sokolowska I, Ngounou Wetie AG, Channaveerappa D, Dupree EJ, Jayathirtha M, Aslebagh R, Wormwood KL, Darie CC. Mass Spectrometry for Proteomics-Based Investigation. Advances in Experimental Medicine and Biology 2019; 1140:1-26. [DOI: 10.1007/978-3-030-15950-4_1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Rao G, Nkepang G, Xu J, Yari H, Houson H, Teng C, Awasthi V. Ubiquitin Receptor RPN13 Mediates the Inhibitory Interaction of Diphenyldihaloketones CLEFMA and EF24 With the 26S Proteasome. Front Chem 2018; 6:392. [PMID: 30280096 PMCID: PMC6153970 DOI: 10.3389/fchem.2018.00392] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 08/13/2018] [Indexed: 11/24/2022] Open
Abstract
The proteasome is a validated target in drug discovery for diseases associated with unusual proteasomal activity. Here we report that two diphenyldihaloketones, CLEFMA and EF24, inhibit the peptidase activity of the 26S proteasome. The objective of this study was to investigate interaction of these compounds with the proteasome and identify a putative target within the protein components of the 26S proteasome. We employed standard fluorogenic peptide-based proteasome activity assay for trypsin-like, chymotrypsin-like, and caspase-like activities of human purified 26S proteasome in cell-free conditions. GFPu-1 and HUVEC cells were used as proteasome reporter cells. Direct binding studies used purified 19S, 20S, 26S, and recombinant RPN13-Pru for interaction with biotinylated analogs of CLEFMA and EF24. The reaction mixtures were subjected to horizontal gel electrophoresis, streptavidin-blotting, pull-down assays, and immunoblotting. The identity of the interacting protein was determined by 2D gel electrophoresis and LC-MS/MS. Drug affinity responsive target stability technique was utilized to examine if CLEFMA binding confers protection to RPN13 against thermolysin-catalyzed proteolysis. We found that trypsin-and chymotrypsin-like activities of the 26S proteasome were reduced significantly by both compounds. The compounds also reduced the proteolytic activity in GFPu-1 and HUVEC cells, resulting in accumulation of ubiquitinated proteins without affecting the autophagy process. From direct binding assays a 43 kDa protein in the 26S proteasome was found to be the interacting partner. This protein was identified by tandem mass spectroscopy as regulatory particle subunit 13 (RPN13), a ubiquitin receptor in the 19S regulatory particle. Furthermore, binding of CLEFMA to RPN13 did not protect latter from thermolysin-mediated proteolysis. Together, this study showed diphenyldihaloketones as potential proteasome inhibitors for treatment of diseases with perturbed proteasome function. The results also unraveled RPN13 as a unique target of CLEFMA and EF24. As a result, these compounds inhibit both trypsin-like and chymotrypsin-like proteasome activities.
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Affiliation(s)
- Geeta Rao
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Gregory Nkepang
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Jian Xu
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Hooman Yari
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Hailey Houson
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Chengwen Teng
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Vibhudutta Awasthi
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
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10
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Vogler BW, Starkenburg SR, Sudasinghe N, Schambach JY, Rollin JA, Pattathil S, Barry AN. Characterization of plant carbon substrate utilization by Auxenochlorella protothecoides. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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11
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López-Coral A, Striz AC, Tuma PL. A Serine/Threonine Kinase 16-Based Phospho-Proteomics Screen Identifies WD Repeat Protein-1 As A Regulator Of Constitutive Secretion. Sci Rep 2018; 8:13049. [PMID: 30158666 DOI: 10.1038/s41598-018-31426-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 08/14/2018] [Indexed: 01/03/2023] Open
Abstract
The plasma membrane of polarized hepatocytes is functionally divided into two domains: the apical and basolateral. Our focus is to define the molecular basis of polarized protein sorting of newly-synthesized membrane and secretory proteins in WIF-B cells, an excellent model system for polarized hepatocytes. We determined that MAL2 (myelin and lymphocyte protein 2) and its binding partner, serine/threonine kinase 16 (STK16) regulate basolateral constitutive secretion. Because STK16 is a constitutively active kinase, we reasoned that constitutively phosphorylated substrates must participate in constitutive secretion. To identify either STK16 substrates or other proteins that regulate constitutive secretion, we took a proteomics approach. Post-nuclear supernatants from cells expressing wild type or a kinase-dead (E202A) STK16 were separated on 2D gels and immunoblotted with antibodies against phospho-serine/threonine residues. Sixteen spots were identified from E202A-expressing cells that reproducibly displayed decreased immunoreactivity. From these spots, 28 proteins were identified as possible STK16 substrates. Out of these 28 possible substrates, 25% of them encode predicted STK16 phosphorylation consensus sites, with WD repeat containing protein-1 (WDR1) encoding two such sites. Based on this finding and on the finding that actin remodeling is required for hepatic secretion, we further confirmed that WDR1 is a phosphoprotein that regulates secretion.
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12
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Bastounis EE, Yeh YT, Theriot JA. Matrix stiffness modulates infection of endothelial cells by Listeria monocytogenes via expression of cell surface vimentin. Mol Biol Cell 2018; 29:1571-1589. [PMID: 29718765 PMCID: PMC6080647 DOI: 10.1091/mbc.e18-04-0228] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Extracellular matrix stiffness (ECM) is one of the many mechanical forces acting on mammalian adherent cells and an important determinant of cellular function. While the effect of ECM stiffness on many aspects of cellular behavior has been studied previously, how ECM stiffness might mediate susceptibility of host cells to infection by bacterial pathogens is hitherto unexplored. To address this open question, we manufactured hydrogels of varying physiologically relevant stiffness and seeded human microvascular endothelial cells (HMEC-1) on them. We then infected HMEC-1 with the bacterial pathogen Listeria monocytogenes (Lm) and found that adhesion of Lm to host cells increases monotonically with increasing matrix stiffness, an effect that requires the activity of focal adhesion kinase (FAK). We identified cell surface vimentin as a candidate surface receptor mediating stiffness-dependent adhesion of Lm to HMEC-1 and found that bacterial infection of these host cells is decreased when the amount of surface vimentin is reduced. Our results provide the first evidence that ECM stiffness can mediate the susceptibility of mammalian host cells to infection by a bacterial pathogen.
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Affiliation(s)
- Effie E Bastounis
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305
| | - Yi-Ting Yeh
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093
| | - Julie A Theriot
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305
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Wormwood KL, Ngounou Wetie AG, Gomez MV, Ju Y, Kowalski P, Mihasan M, Darie CC. Structural Characterization and Disulfide Assignment of Spider Peptide Phα1β by Mass Spectrometry. J Am Soc Mass Spectrom 2018; 29:827-841. [PMID: 29663255 DOI: 10.1007/s13361-018-1904-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 01/19/2018] [Accepted: 01/22/2018] [Indexed: 06/08/2023]
Abstract
Native Phα1β is a peptide purified from the venom of the armed spider Phoneutria nigriventer that has been shown to have an extensive analgesic effect with fewer side effects than ω-conotoxin MVIIA. Recombinant Phα1β mimics the effects of the native Phα1β. Because of this, it has been suggested that Phα1β may have potential to be used as a therapeutic for controlling persistent pathological pain. The amino acid sequence of Phα1β is known; however, the exact structure and disulfide arrangement has yet to be determined. Determination of the disulfide linkages and exact structure could greatly assist in pharmacological analysis and determination of why this peptide is such an effective analgesic. Here, we used biochemical and mass spectrometry approaches to determine the disulfide linkages present in the recombinant Phα1β peptide. Using a combination of MALDI-MS, direct infusion ESI-MS, and nanoLC-MS/MS analysis of the undigested recombinant Phα1β peptide and digested with AspN, trypsin, or AspN/trypsin, we were able to identify and confirm all six disulfide linkages present in the peptide as Cys1-2, Cys3-4, Cys5-6, Cys7-8, Cys9-10, and Cys11-12. These results were also partially confirmed in the native Phα1β peptide. These experiments provide essential structural information about Phα1β and may assist in providing insight into the peptide's analgesic effect with very low side effects. Graphical Abstract ᅟ.
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Affiliation(s)
- Kelly L Wormwood
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, 8 Clarkson Ave., Box 5810, Potsdam, NY, 13699, USA
| | - Armand Gatien Ngounou Wetie
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, 8 Clarkson Ave., Box 5810, Potsdam, NY, 13699, USA
| | - Marcus Vinicius Gomez
- Institute of Education and Research Santa Casa Belo Horizonte-Laboratory of Toxins, Rua Domingos Vieira 590, Belo Horizonte, Minas Gerais, 30150-240, Brazil
| | - Yue Ju
- Bruker Daltonics, 40 Manning Road Manning Park, Billerica, MA, 01821, USA
| | - Paul Kowalski
- Bruker Daltonics, 40 Manning Road Manning Park, Billerica, MA, 01821, USA
| | - Marius Mihasan
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, 8 Clarkson Ave., Box 5810, Potsdam, NY, 13699, USA
- Department of Biology, Alexandru Ioan Cuza University of Iasi, Carol I Bvd. no 11, 700506, Iasi, Romania
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, 8 Clarkson Ave., Box 5810, Potsdam, NY, 13699, USA.
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Channaveerappa D, Lux JC, Wormwood KL, Heintz TA, McLerie M, Treat JA, King H, Alnasser D, Goodrow RJ, Ballard G, Decker R, Darie CC, Panama BK. Atrial electrophysiological and molecular remodelling induced by obstructive sleep apnoea. J Cell Mol Med 2017; 21:2223-2235. [PMID: 28402037 PMCID: PMC5571519 DOI: 10.1111/jcmm.13145] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 01/31/2017] [Indexed: 12/19/2022] Open
Abstract
Obstructive sleep apnoea (OSA) affects 9-24% of the adult population. OSA is associated with atrial disease, including atrial enlargement, fibrosis and arrhythmias. Despite the link between OSA and cardiac disease, the molecular changes in the heart which occur with OSA remain elusive. To study OSA-induced cardiac changes, we utilized a recently developed rat model which closely recapitulates the characteristics of OSA. Male Sprague Dawley rats, aged 50-70 days, received surgically implanted tracheal balloons which were inflated to cause transient airway obstructions. Rats were given 60 apnoeas per hour of either 13 sec. (moderate apnoea) or 23 sec. (severe apnoea), 8 hrs per day for 2 weeks. Controls received implants, but no inflations were made. Pulse oximetry measurements were taken at regular intervals, and post-apnoea ECGs were recorded. Rats had longer P wave durations and increased T wave amplitudes following chronic OSA. Proteomic analysis of the atrial tissue homogenates revealed that three of the nine enzymes in glycolysis, and two proteins related to oxidative phosphorylation, were down regulated in the severe apnoea group. Several sarcomeric and pro-hypertrophic proteins were also up regulated with OSA. Chronic OSA causes proteins changes in the atria which suggest impairment of energy metabolism and enhancement of hypertrophy.
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Affiliation(s)
- Devika Channaveerappa
- Biochemistry and Proteomics GroupDepartment of Chemistry and Biomolecular ScienceClarkson UniversityPotsdamNYUSA
| | - Jacob C. Lux
- Department of Experimental CardiologyMasonic Medical Research LaboratoryUticaNYUSA
| | - Kelly L. Wormwood
- Biochemistry and Proteomics GroupDepartment of Chemistry and Biomolecular ScienceClarkson UniversityPotsdamNYUSA
| | - Timothy A. Heintz
- Department of Experimental CardiologyMasonic Medical Research LaboratoryUticaNYUSA
| | - Meredith McLerie
- Department of Experimental CardiologyMasonic Medical Research LaboratoryUticaNYUSA
| | - Jacqueline A. Treat
- Department of Experimental CardiologyMasonic Medical Research LaboratoryUticaNYUSA
| | - Hannah King
- Department of Experimental CardiologyMasonic Medical Research LaboratoryUticaNYUSA
| | - Donia Alnasser
- Department of Experimental CardiologyMasonic Medical Research LaboratoryUticaNYUSA
| | - Robert J. Goodrow
- Department of Experimental CardiologyMasonic Medical Research LaboratoryUticaNYUSA
| | - Glenn Ballard
- Electrical Engineering TechnologyMohawk Valley Community CollegeUticaNYUSA
| | - Robert Decker
- Electrical Engineering TechnologyMohawk Valley Community CollegeUticaNYUSA
| | - Costel C. Darie
- Biochemistry and Proteomics GroupDepartment of Chemistry and Biomolecular ScienceClarkson UniversityPotsdamNYUSA
| | - Brian K. Panama
- Department of Experimental CardiologyMasonic Medical Research LaboratoryUticaNYUSA
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15
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Müller T, Winter D. Systematic Evaluation of Protein Reduction and Alkylation Reveals Massive Unspecific Side Effects by Iodine-containing Reagents. Mol Cell Proteomics 2017; 16:1173-1187. [PMID: 28539326 DOI: 10.1074/mcp.m116.064048] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 05/23/2017] [Indexed: 12/27/2022] Open
Abstract
Reduction and alkylation of cysteine residues is part of virtually any proteomics workflow. Despite its frequent use, up to date no systematic investigation of the impact of different conditions on the outcome of proteomics studies has been performed. In this study, we compared common reduction reagents (dithiothreitol, tris-(2-carboxyethyl)-phosphine, and β-mercaptoethanol) and alkylation reagents (iodoacetamide, iodoacetic acid, acrylamide, and chloroacetamide). Using in-gel digests as well as SAX fractionated in-solution digests of cytosolic fractions of HeLa cells, we evaluated 13 different reduction and alkylation conditions resulting in considerably varying identification rates. We observed strong differences in offsite alkylation reactions at 7 amino acids as well as at the peptide N terminus, identifying single and double adducts of all reagents. Using dimethyl labeling, mass tolerant searches, and synthetic peptide experiments, we identified alkylation of methionine residues by iodine-containing alkylation reagents as one of the major factors for the differences. We observed differences of more than 9-fold in numbers of identified methionine-containing peptide spectral matches for in-gel digested samples between iodine- and noniodine-containing alkylation reagents. This was because of formation of carbamidomethylated and carboxymethylated methionine side chains and a resulting prominent neutral loss during ESI ionization or in MS/MS fragmentation, strongly decreasing identification rates of methionine-containing peptides. We achieved best results with acrylamide as alkylation reagent, whereas the highest numbers of peptide spectral matches were obtained when reducing with dithiothreitol and β-mercaptoethanol for the in-solution and the in-gel digested samples, respectively.
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Affiliation(s)
- Torsten Müller
- From the ‡Institute for Biochemistry and Molecular Biology, University of Bonn, Germany
| | - Dominic Winter
- From the ‡Institute for Biochemistry and Molecular Biology, University of Bonn, Germany
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Tome ME, Schaefer CP, Jacobs LM, Zhang Y, Herndon JM, Matty FO, Davis TP. Identification of P-glycoprotein co-fractionating proteins and specific binding partners in rat brain microvessels. J Neurochem 2015; 134:200-10. [PMID: 25832806 DOI: 10.1111/jnc.13106] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 02/26/2015] [Accepted: 03/23/2015] [Indexed: 11/27/2022]
Abstract
Drug delivery to the brain for the treatment of pathologies with a CNS component is a significant clinical challenge. P-glycoprotein (PgP), a drug efflux pump in the endothelial cell membrane, is a major factor in preventing therapeutics from crossing the blood-brain barrier (BBB). Identifying PgP regulatory mechanisms is key to developing agents to modulate PgP activity. Previously, we found that PgP trafficking was altered concomitant with increased PgP activity and disassembly of high molecular weight PgP-containing complexes during acute peripheral inflammatory pain. These data suggest that PgP activity is post-translationally regulated at the BBB. The goal of the current study was to identify proteins that co-localize with PgP in rat brain microvessel endothelial cell membrane microdomains and use the data to suggest potential regulatory mechanisms. Using new density gradients of microvessel homogenates, we identified two unique pools (1,2) of PgP in membrane fractions. Caveolar constituents, caveolin1, cavin1, and cavin2, co-localized with PgP in these fractions indicating the two pools contained caveolae. A chaperone (Hsc71), protein disulfide isomerase and endosomal/lysosomal sorting proteins (Rab5, Rab11a) also co-fractionated with PgP in the gradients. These data suggest signaling pathways with a potential role in post-translational regulation of PgP activity at the BBB.
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Affiliation(s)
- Margaret E Tome
- Department of Medical Pharmacology, University of Arizona, Tucson, Arizona, USA
| | - Charles P Schaefer
- Department of Medical Pharmacology, University of Arizona, Tucson, Arizona, USA
| | - Leigh M Jacobs
- Department of Medical Pharmacology, University of Arizona, Tucson, Arizona, USA
| | - Yifeng Zhang
- Department of Medical Pharmacology, University of Arizona, Tucson, Arizona, USA
| | - Joseph M Herndon
- Department of Medical Pharmacology, University of Arizona, Tucson, Arizona, USA
| | - Fabian O Matty
- Department of Medical Pharmacology, University of Arizona, Tucson, Arizona, USA
| | - Thomas P Davis
- Department of Medical Pharmacology, University of Arizona, Tucson, Arizona, USA
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Baral R, Ngounou Wetie AG, Darie CC, Wallace KN. Mass spectrometry for proteomics-based investigation using the zebrafish vertebrate model system. Adv Exp Med Biol 2014; 806:331-40. [PMID: 24952190 DOI: 10.1007/978-3-319-06068-2_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The zebrafish (Danio rerio) is frequently being used to investigate the genetics of human diseases as well as resulting pathologies. Ease of both forward and reverse genetic manipulation along with conservation of vertebrate organ systems and disease causing genes has made this system a popular model. Many techniques have been developed to manipulate the genome of zebrafish producing mutants in a vast array of genes. While genetic manipulation of zebrafish has progressed, proteomics have been under-utilized. This review highlights studies that have already been performed using proteomic techniques and as well as our initial proteomic work comparing changes to the proteome between the ascl1a-/- and WT intestine.
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Affiliation(s)
- Reshica Baral
- Department of Biology, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, 13699-5810, USA
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Ngounou Wetie AG, Wormwood K, Thome J, Dudley E, Taurines R, Gerlach M, Woods AG, Darie CC. A pilot proteomic study of protein markers in autism spectrum disorder. Electrophoresis 2014; 35:2046-54. [DOI: 10.1002/elps.201300370] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 02/20/2014] [Accepted: 03/19/2014] [Indexed: 12/14/2022]
Affiliation(s)
- Armand G. Ngounou Wetie
- Department of Chemistry and Biomolecular Science; Biochemistry and Proteomics Group; Clarkson University; Potsdam NY USA
| | - Kelly Wormwood
- Department of Chemistry and Biomolecular Science; Biochemistry and Proteomics Group; Clarkson University; Potsdam NY USA
| | - Johannes Thome
- Department of Psychiatry; University of Rostock; Rostock Germany
- College of Medicine; Swansea University; Swansea UK
| | | | - Regina Taurines
- Department of Child and Adolescent Psychiatry; Psychosomatics and Psychotherapy; University of Würzburg; Germany
| | - Manfred Gerlach
- Department of Child and Adolescent Psychiatry; Psychosomatics and Psychotherapy; University of Würzburg; Germany
| | - Alisa G. Woods
- Department of Chemistry and Biomolecular Science; Biochemistry and Proteomics Group; Clarkson University; Potsdam NY USA
| | - Costel C. Darie
- Department of Chemistry and Biomolecular Science; Biochemistry and Proteomics Group; Clarkson University; Potsdam NY USA
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Sandu C, Wetie AGN, Darie CC, Steller H. Thiostrepton, a Natural Compound That Triggers Heat Shock Response and Apoptosis in Human Cancer Cells: A Proteomics Investigation. Advances in Experimental Medicine and Biology 2014. [DOI: 10.1007/978-3-319-06068-2_21] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Woods AG, Sokolowska I, Ngounou Wetie AG, Wormwood K, Aslebagh R, Patel S, Darie CC. Mass spectrometry for proteomics-based investigation. Adv Exp Med Biol 2014; 806:1-32. [PMID: 24952176 DOI: 10.1007/978-3-319-06068-2_1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Within the past years, we have witnessed a great improvement in mass spectrometry (MS) and proteomics approaches in terms of instrumentation, protein fractionation, and bioinformatics. With the current technology, protein identification alone is no longer sufficient. Both scientists and clinicians want not only to identify proteins but also to identify the protein's posttranslational modifications (PTMs), protein isoforms, protein truncation, protein-protein interaction (PPI), and protein quantitation. Here, we describe the principle of MS and proteomics and strategies to identify proteins, protein's PTMs, protein isoforms, protein truncation, PPIs, and protein quantitation. We also discuss the strengths and weaknesses within this field. Finally, in our concluding remarks we assess the role of mass spectrometry and proteomics in scientific and clinical settings in the near future. This chapter provides an introduction and overview for subsequent chapters that will discuss specific MS proteomic methodologies and their application to specific medical conditions. Other chapters will also touch upon areas that expand beyond proteomics, such as lipidomics and metabolomics.
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Affiliation(s)
- Alisa G Woods
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, 13699-5810, USA
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Woods AG, Sokolowska I, Deinhardt K, Darie CC. Investigating a Novel Protein Using Mass Spectrometry: The Example of Tumor Differentiation Factor (TDF). Advances in Experimental Medicine and Biology 2014; 806:509-23. [DOI: 10.1007/978-3-319-06068-2_25] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Patel S, Ngounou Wetie AG, Darie CC, Clarkson BD. Cancer secretomes and their place in supplementing other hallmarks of cancer. Adv Exp Med Biol 2014; 806:409-42. [PMID: 24952195 DOI: 10.1007/978-3-319-06068-2_20] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The secretome includes all macromolecules secreted by cells, in particular conditions at defined times, allowing cell-cell communication. Cancer cell secretomes that are altered compared to normal cells have shown significant potential for elucidating cancer biology. Proteins of secretomes are secreted by various secretory pathways and can be studied using different methods. Cancer secretomes seem to play an important role in known hallmarks of cancers such as excessive proliferation, reduced apoptosis, immune invasion, angioneogenesis, alteration in energy metabolism, and development of resistance against anti-cancer therapy [1, 2]. If a significant role of an altered secretome can be identified in cancer cells, using advanced mass spectrometry-based techniques, this may allow researchers to screen and characterize the secretome proteins involved in cancer progression and open up new opportunities to develop new therapies. We aim to elaborate upon recent advances in cancer cell secretome analysis using different proteomics techniques. In this review, we highlight the role of the altered secretome in contributing to already recognized and emerging hallmarks of cancer and we discuss new challenges in the field of secretome analysis.
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Affiliation(s)
- Sapan Patel
- Memorial Sloan Kettering Cancer Center, Molecular Pharmacology and Chemistry Program, 415 East 68th Street, New York, NY, 10065, USA
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Abstract
Major depressive disorder (MDD) is common. Despite numerous available treatments, many individuals fail to improve clinically. MDD continues to be diagnosed exclusively via behavioral rather than biological methods. Biomarkers-which include measurements of genes, proteins, and patterns of brain activity-may provide an important objective tool for the diagnosis of MDD or in the rational selection of treatments. Proteomic analysis and validation of its results as biomarkers is less explored than other areas of biomarker research in MDD. Mass spectrometry (MS) is a comprehensive, unbiased means of proteomic analysis, which can be complemented by directed protein measurements, such as Western Blotting. Prior studies have focused on MS analysis of several human biomaterials in MDD, including human post-mortem brain, cerebrospinal fluid (CSF), blood components, and urine. Further studies utilizing MS and proteomic analysis in MDD may help solidify and establish biomarkers for use in diagnosis, identification of new treatment targets, and understanding of the disorder. The ultimate goal is the validation of a biomarker or a biomarker signature that facilitates a convenient and inexpensive predictive test for depression treatment response and helps clinicians in the rational selection of next-step treatments.
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Ngounou Wetie AG, Dekroon RM, Mocanu M, Ryan JP, Darie CC, Woods AG. Mass spectrometry for the study of autism and neurodevelopmental disorders. Adv Exp Med Biol 2014; 806:525-44. [PMID: 24952201 DOI: 10.1007/978-3-319-06068-2_26] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Mass spectrometry (MS) has been increasingly used to study central nervous system disorders, including autism spectrum disorders (ASDs). The first studies of ASD using MS focused on the identification of external toxins, but current research is more directed at understanding endogenous protein changes that occur in ASD (ASD proteomics). This chapter focuses on how MS has been used to study ASDs, with particular focus on proteomic analysis. Other neurodevelopmental disorders have been investigated using this technique, including genetic syndromes associated with autism such as fragile X syndrome and Smith-Lemli-Opitz syndrome.
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Wetie AGN, Woods AG, Darie CC. Mass Spectrometric Analysis of Post-translational Modifications (PTMs) and Protein–Protein Interactions (PPIs). Advances in Experimental Medicine and Biology 2014. [DOI: 10.1007/978-3-319-06068-2_9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Sokolowska I, Ngounou Wetie AG, Wormwood K, Thome J, Darie CC, Woods AG. The potential of biomarkers in psychiatry: focus on proteomics. J Neural Transm (Vienna) 2015; 122:9-18. [DOI: 10.1007/s00702-013-1134-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 12/02/2013] [Indexed: 02/06/2023]
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Petrareanu C, Macovei A, Sokolowska I, Woods AG, Lazar C, Radu GL, Darie CC, Branza-Nichita N. Comparative proteomics reveals novel components at the plasma membrane of differentiated HepaRG cells and different distribution in hepatocyte- and biliary-like cells. PLoS One 2013; 8:e71859. [PMID: 23977166 PMCID: PMC3748114 DOI: 10.1371/journal.pone.0071859] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 07/04/2013] [Indexed: 12/11/2022] Open
Abstract
Hepatitis B virus (HBV) is a human pathogen causing severe liver disease and eventually death. Despite important progress in deciphering HBV internalization, the early virus-cell interactions leading to infection are not known. HepaRG is a human bipotent liver cell line bearing the unique ability to differentiate towards a mixture of hepatocyte- and biliary-like cells. In addition to expressing metabolic functions normally found in liver, differentiated HepaRG cells support HBV infection in vitro, thus resembling cultured primary hepatocytes more than other hepatoma cells. Therefore, extensive characterization of the plasma membrane proteome from HepaRG cells would allow the identification of new cellular factors potentially involved in infection. Here we analyzed the plasma membranes of non-differentiated and differentiated HepaRG cells using nanoliquid chromatography-tandem mass spectrometry to identify the differences between the proteomes and the changes that lead to differentiation of these cells. We followed up on differentially-regulated proteins in hepatocytes- and biliary-like cells, focusing on Cathepsins D and K, Cyclophilin A, Annexin 1/A1, PDI and PDI A4/ERp72. Major differences between the two proteomes were found, including differentially regulated proteins, protein-protein interactions and intracellular localizations following differentiation. The results advance our current understanding of HepaRG differentiation and the unique properties of these cells.
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Affiliation(s)
- Catalina Petrareanu
- Department of Viral Glycoproteins, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
- Department of Analytical Chemistry and Enviromental Engineering, Faculty of Applied Chemistry and Materials Science, Politehnica University of Bucharest, Bucharest, Romania
| | - Alina Macovei
- Department of Viral Glycoproteins, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Izabela Sokolowska
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York, United States of America
| | - Alisa G. Woods
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York, United States of America
| | - Catalin Lazar
- Department of Viral Glycoproteins, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Gabriel L. Radu
- Department of Analytical Chemistry and Enviromental Engineering, Faculty of Applied Chemistry and Materials Science, Politehnica University of Bucharest, Bucharest, Romania
| | - Costel C. Darie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York, United States of America
| | - Norica Branza-Nichita
- Department of Viral Glycoproteins, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
- * E-mail:
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Sokolowska I, Ngounou Wetie AG, Roy U, Woods AG, Darie CC. Mass spectrometry investigation of glycosylation on the NXS/T sites in recombinant glycoproteins. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2013; 1834:1474-83. [DOI: 10.1016/j.bbapap.2013.04.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Revised: 04/15/2013] [Accepted: 04/22/2013] [Indexed: 01/17/2023]
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Ngounou Wetie AG, Sokolowska I, Wormwood K, Beglinger K, Michel TM, Thome J, Darie CC, Woods AG. Mass spectrometry for the detection of potential psychiatric biomarkers. J Mol Psychiatry 2013; 1:8. [PMID: 25408901 PMCID: PMC4223884 DOI: 10.1186/2049-9256-1-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 02/12/2013] [Indexed: 12/20/2022] Open
Abstract
The search for molecules that can act as potential biomarkers is increasing in the scientific community, including in the field of psychiatry. The field of proteomics is evolving and its indispensability for identifying biomarkers is clear. Among proteomic tools, mass spectrometry is the core technique for qualitative and quantitative identification of protein markers. While significant progress has been made in the understanding of biomarkers for neurodegenerative diseases such as Alzheimer's disease, multiple sclerosis and Parkinson's disease, psychiatric disorders have not been as extensively investigated. Recent and successful applications of mass spectrometry-based proteomics in fields such as cardiovascular disease, cancer, infectious diseases and neurodegenerative disorders suggest a similar path for psychiatric disorders. In this brief review, we describe mass spectrometry and its use in psychiatric biomarker research and highlight some of the possible challenges of undertaking this type of work. Further, specific examples of candidate biomarkers are highlighted. A short comparison of proteomic with genomic methods for biomarker discovery research is presented. In summary, mass spectrometry-based techniques may greatly facilitate ongoing efforts to understand molecular mechanisms of psychiatric disorders.
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Affiliation(s)
- Armand G Ngounou Wetie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Izabela Sokolowska
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Kelly Wormwood
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Katherine Beglinger
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Tanja Maria Michel
- Department of Psychiatry, University of Rostock, Rostock, Gehlsheimer Straße 20, D-18147 Germany
| | - Johannes Thome
- Department of Psychiatry, University of Rostock, Rostock, Gehlsheimer Straße 20, D-18147 Germany ; College of Medicine, Swansea University, Singleton Park, Swansea, SA2 8PP UK
| | - Costel C Darie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Alisa G Woods
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA ; Neuropsychology Clinic and Psychoeducation Services, SUNY Plattsburgh, 101 Broad St, Plattsburgh, 12901 NY USA
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Woods AG, Ngounou Wetie AG, Sokolowska I, Russell S, Ryan JP, Michel TM, Thome J, Darie CC. Mass spectrometry as a tool for studying autism spectrum disorder. J Mol Psychiatry 2013; 1:6. [PMID: 25408899 PMCID: PMC4223881 DOI: 10.1186/2049-9256-1-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 11/13/2012] [Indexed: 12/04/2022] Open
Abstract
Autism spectrum disorders (ASDs) are increasing in incidence but have an incompletely understood etiology. Tools for uncovering clues to the cause of ASDs and means for diagnoses are valuable to the field. Mass Spectrometry (MS) has been a useful method for evaluating differences between individuals with ASDs versus matched controls. Different biological substances can be evaluated using MS, including urine, blood, saliva, and hair. This technique has been used to evaluate relatively unsupported hypotheses based on introduction of exogenous factors, such as opiate and heavy metal excretion theories of ASDs. MS has also been used to support disturbances in serotonin-related molecules, which have been more consistently observed in ASDs. Serotonergic system markers, markers for oxidative stress, cholesterol system disturbances, peptide hypo-phosphorylation and methylation have been measured using MS in ASDs, although further analyses with larger numbers of subjects are needed (as well as consideration of behavioral data). Refinements in MS and data analysis are ongoing, allowing for the possibility that future studies examining body fluids and specimens from ASD subjects could continue to yield novel insights. This review summarizes MS investigations that have been conducted to study ASD to date and provides insight into future promising applications for this technique, with focus on proteomic studies.
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Affiliation(s)
- Alisa G Woods
- Biochemistry and Proteomics Group Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Armand G Ngounou Wetie
- Biochemistry and Proteomics Group Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Izabela Sokolowska
- Biochemistry and Proteomics Group Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Stefanie Russell
- Department of Psychology, State University of New York at Plattsburgh, 101 Broad Street, Plattsburgh, NY 12901 USA
| | - Jeanne P Ryan
- Department of Psychology, State University of New York at Plattsburgh, 101 Broad Street, Plattsburgh, NY 12901 USA
| | - Tanja Maria Michel
- Department of Psychiatry, University of Rostock, Gehlsheimer Straße 20, D-18147 Rostock, Germany
| | - Johannes Thome
- Department of Psychiatry, University of Rostock, Gehlsheimer Straße 20, D-18147 Rostock, Germany ; College of Medicine, Swansea University, Singleton Park, Swansea, SA2 8PP UK
| | - Costel C Darie
- Biochemistry and Proteomics Group Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
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Ngounou Wetie AG, Sokolowska I, Woods AG, Roy U, Deinhardt K, Darie CC. Protein–protein interactions: switch from classical methods to proteomics and bioinformatics-based approaches. Cell Mol Life Sci 2013; 71:205-28. [DOI: 10.1007/s00018-013-1333-1] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Revised: 03/25/2013] [Accepted: 03/26/2013] [Indexed: 11/28/2022]
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Ngounou Wetie AG, Sokolowska I, Woods AG, Roy U, Loo JA, Darie CC. Investigation of stable and transient protein-protein interactions: Past, present, and future. Proteomics 2013. [PMID: 23193082 DOI: 10.1002/pmic.201200328] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
This article presents an overview of the literature and a review of recent advances in the analysis of stable and transient protein-protein interactions (PPIs) with a focus on their function within cells, organs, and organisms. The significance of PTMs within the PPIs is also discussed. We focus on methods to study PPIs and methods of detecting PPIs, with particular emphasis on electrophoresis-based and MS-based investigation of PPIs, including specific examples. The validation of PPIs is emphasized and the limitations of the current methods for studying stable and transient PPIs are discussed. Perspectives regarding PPIs, with focus on bioinformatics and transient PPIs are also provided.
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Affiliation(s)
- Armand G Ngounou Wetie
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
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Abstract
Deciphering the biological and clinical significance of the proteins is investigated by mass spectrometry in a relatively new field, named proteomics. Mass spectrometry is, however, also used in chemistry for many years. In this Research Front we try to show the potential use of mass spectrometry in chemical, environmental and biomedical research and also to illustrate the applications of mass spectrometry in proteomics.
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Abstract
Characterisation of proteins and whole proteomes can provide a foundation to our understanding of physiological and pathological states and biological diseases or disorders. Constant development of more reliable and accurate mass spectrometry (MS) instruments and techniques has allowed for better identification and quantification of the thousands of proteins involved in basic physiological processes. Therefore, MS-based proteomics has been widely applied to the analysis of biological samples and has greatly contributed to our understanding of protein functions, interactions, and dynamics, advancing our knowledge of cellular processes as well as the physiology and pathology of the human body. This review will discuss current proteomic approaches for protein identification and characterisation, including post-translational modification (PTM) analysis and quantitative proteomics as well as investigation of protein–protein interactions (PPIs).
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Abstract
Proteins are the effector molecules of many cellular and biological processes and are thus very dynamic and flexible. Regulation of protein activity, structure, stability, and turnover is in part controlled by their post-translational modifications (PTMs). Common PTMs of proteins include phosphorylation, glycosylation, methylation, ubiquitination, acetylation, and oxidation. Understanding the biology of protein PTMs can help elucidate the mechanisms of many pathological conditions and provide opportunities for prevention, diagnostics, and treatment of these disorders. Prior to the era of proteomics, it was standard to use chemistry methods for the identification of protein modifications. With advancements in proteomic technologies, mass spectrometry has become the method of choice for the analysis of protein PTMs. In this brief review, we will highlight the biochemistry of PTMs with an emphasis on mass spectrometry.
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Sokolowska I, Woods AG, Gawinowicz MA, Roy U, Darie CC. Characterization of tumor differentiation factor (TDF) and its receptor (TDF-R). Cell Mol Life Sci 2013; 70:2835-48. [DOI: 10.1007/s00018-012-1185-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 09/27/2012] [Accepted: 10/01/2012] [Indexed: 10/27/2022]
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