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DeBlasio SL, Wilson JR, Tamborindeguy C, Johnson RS, Pinheiro PV, MacCoss MJ, Gray SM, Heck M. Affinity Purification-Mass Spectrometry Identifies a Novel Interaction between a Polerovirus and a Conserved Innate Immunity Aphid Protein that Regulates Transmission Efficiency. J Proteome Res 2021; 20:3365-3387. [PMID: 34019426 DOI: 10.1021/acs.jproteome.1c00313] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The vast majority of plant viruses are transmitted by insect vectors, with many crucial aspects of the transmission process being mediated by key protein-protein interactions. Still, very few vector proteins interacting with viruses have been identified and functionally characterized. Potato leafroll virus (PLRV) is transmitted most efficiently by Myzus persicae, the green peach aphid, in a circulative, non-propagative manner. Using affinity purification coupled to high-resolution mass spectrometry (AP-MS), we identified 11 proteins from M. persicaedisplaying a high probability of interaction with PLRV and an additional 23 vector proteins with medium confidence interaction scores. Three of these aphid proteins were confirmed to directly interact with the structural proteins of PLRV and other luteovirid species via yeast two-hybrid. Immunolocalization of one of these direct PLRV-interacting proteins, an orthologue of the human innate immunity protein complement component 1 Q subcomponent-binding protein (C1QBP), shows that MpC1QBP partially co-localizes with PLRV in cytoplasmic puncta and along the periphery of aphid gut epithelial cells. Artificial diet delivery to aphids of a chemical inhibitor of C1QBP leads to increased PLRV acquisition by aphids and subsequently increased titer in inoculated plants, supporting a role for C1QBP in the acquisition and transmission efficiency of PLRV by M. persicae. This study presents the first use of AP-MS for the in vivo isolation of a functionally relevant insect vector-virus protein complex. MS data are available from ProteomeXchange.org using the project identifier PXD022167.
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Affiliation(s)
- Stacy L DeBlasio
- Emerging Pests and Pathogens Research Unit, USDA Agricultural Research Service, Ithaca, New York 14853, United States.,Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, United States
| | - Jennifer R Wilson
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, United States.,Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853, United States
| | - Cecilia Tamborindeguy
- Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853, United States
| | - Richard S Johnson
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
| | - Patricia V Pinheiro
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, United States.,Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853, United States
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
| | - Stewart M Gray
- Emerging Pests and Pathogens Research Unit, USDA Agricultural Research Service, Ithaca, New York 14853, United States.,Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853, United States
| | - Michelle Heck
- Emerging Pests and Pathogens Research Unit, USDA Agricultural Research Service, Ithaca, New York 14853, United States.,Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, United States.,Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853, United States
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Sweet C, Aayush A, Readnour L, Solomon KV, Thompson DH. Development of a Fast Organic Extraction-Precipitation Method for Improved Purification of Elastin-Like Polypeptides That Is Independent of Sequence and Molecular Weight. Biomacromolecules 2021; 22:1990-1998. [PMID: 33826307 PMCID: PMC8496954 DOI: 10.1021/acs.biomac.1c00096] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Elastin-like polypeptides (ELP), an increasingly popular tag for protein purification, commonly rely upon inverse transition cycling (ITC) to exploit their lower critical solution temperature characteristics for purification. While considerably faster than chromatography, ITC is still time consuming and often fails to remove host cell contaminants to an acceptable level for in vivo experiments. Here, we present a rapid purification workflow for ELP of broadly varying molecular weight and sequence using a polar organic solvent extraction and precipitation strategy. Four different ELP purification methods were directly compared for their ability to remove host cell protein, nucleic acids, and lipopolysaccharide (LPS) contaminants using a model ELP. On the basis of these findings, an optimized extraction-precipitation method was developed that gave highly pure ELP from bacterial pellets in approximately 2.5 h while removing major host cell contaminants, including LPS to levels below 1 EU/mL, to produce highly pure material that is suitable for in vivo applications. Application of this method to the rapid purification of an ELP-epidermal growth factor fusion gave an isolate that retained its capacity to bind to epidermal growth factor receptor positive cells, thereby demonstrating that this method is capable of producing a functional construct after purification by organic extraction-precipitation.
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Affiliation(s)
| | | | - Logan Readnour
- Department of Agricultural and Biological Engineering, Purdue University, 1203 West State Street, West Lafayette, Indiana 47907, United States
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Chiconato DA, de Santana Costa MG, Balbuena TS, Munns R, Dos Santos DMM. Proteomic analysis of young sugarcane plants with contrasting salt tolerance. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:588-596. [PMID: 33581744 DOI: 10.1071/fp20314] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/19/2021] [Indexed: 05/20/2023]
Abstract
Soil salinity affects sugarcane (Saccharum officinale L.) production in arid and semiarid climates, severely reducing productivity. This study aimed to identify differentially regulated proteins in two cultivars that differ markedly in tolerance of saline soil. Plants were grown for 30 days and then subjected to treatments of 0 and 160 mM NaCl for 15 days. The tolerant cultivar showed a 3-fold upregulation of lipid metabolising enzymes, GDSL-motif lipases, which are associated with defence to abiotic stress, and which were not upregulated in the sensitive cultivar. Lipoxygenase was 2-fold upregulated in the tolerant cultivar but not in the sensitive cultivar, as were Type III chlorophyll a/b binding proteins. Other differences were that in the sensitive cultivar, the key enzyme of C4 photosynthesis, phosphoenolpyruvate carboxylase was downregulated, along with other chloroplast enzymes. Na+ concentrations had not reached toxic concentrations in either cultivar by this time of exposure to salt, so these changes would be in response to the osmotic effect of the soil salinity, and likely be in common with plants undergoing drought stress.
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Affiliation(s)
- Denise A Chiconato
- Department of Biologia Aplicada à Agropecuária, Universidade Estadual Paulista 'Julio de Mesquita Filho', 14884-900 Jaboticabal, SP, Brasil; and CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Marília G de Santana Costa
- Department of Tecnologia, Universidade Estadual Paulista 'Julio de Mesquita Filho', 14884-900 Jaboticabal, SP, Brasil
| | - Tiago S Balbuena
- Department of Tecnologia, Universidade Estadual Paulista 'Julio de Mesquita Filho', 14884-900 Jaboticabal, SP, Brasil
| | - Rana Munns
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2601, Australia; and School of Agriculture and Environment, and ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, WA 6009, Australia; and Corresponding author.
| | - Durvalina M M Dos Santos
- Department of Biologia Aplicada à Agropecuária, Universidade Estadual Paulista 'Julio de Mesquita Filho', 14884-900 Jaboticabal, SP, Brasil
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Chen JJ, Fan Y, Boehning D. Regulation of Dynamic Protein S-Acylation. Front Mol Biosci 2021; 8:656440. [PMID: 33981723 PMCID: PMC8107437 DOI: 10.3389/fmolb.2021.656440] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 02/16/2021] [Indexed: 12/20/2022] Open
Abstract
Protein S-acylation is the reversible addition of fatty acids to the cysteine residues of target proteins. It regulates multiple aspects of protein function, including the localization to membranes, intracellular trafficking, protein interactions, protein stability, and protein conformation. This process is regulated by palmitoyl acyltransferases that have the conserved amino acid sequence DHHC at their active site. Although they have conserved catalytic cores, DHHC enzymes vary in their protein substrate selection, lipid substrate preference, and regulatory mechanisms. Alterations in DHHC enzyme function are associated with many human diseases, including cancers and neurological conditions. The removal of fatty acids from acylated cysteine residues is catalyzed by acyl protein thioesterases. Notably, S-acylation is now known to be a highly dynamic process, and plays crucial roles in signaling transduction in various cell types. In this review, we will explore the recent findings on protein S-acylation, the enzymatic regulation of this process, and discuss examples of dynamic S-acylation.
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Szafran BN, Borazjani A, Seay CN, Carr RL, Lehner R, Kaplan BLF, Ross MK. Effects of Chlorpyrifos on Serine Hydrolase Activities, Lipid Mediators, and Immune Responses in Lungs of Neonatal and Adult Mice. Chem Res Toxicol 2021; 34:1556-1571. [PMID: 33900070 DOI: 10.1021/acs.chemrestox.0c00488] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chlorpyrifos (CPF) is an organophosphate (OP) pesticide that causes acute toxicity by inhibiting acetylcholinesterase (AChE) in the nervous system. However, endocannabinoid (eCB) metabolizing enzymes in brain of neonatal rats are more sensitive than AChE to inhibition by CPF, leading to increased levels of eCBs. Because eCBs are immunomodulatory molecules, we investigated the association between eCB metabolism, lipid mediators, and immune function in adult and neonatal mice exposed to CPF. We focused on lung effects because epidemiologic studies have linked pesticide exposures to respiratory diseases. CPF was hypothesized to disrupt lung eCB metabolism and alter lung immune responses to lipopolysaccharide (LPS), and these effects would be more pronounced in neonatal mice due to an immature immune system. We first assessed the biochemical effects of CPF in adult mice (≥8 weeks old) and neonatal mice after administering CPF (2.5 mg/kg, oral) or vehicle for 7 days. Tissues were harvested 4 h after the last CPF treatment and lung microsomes from both age groups demonstrated CPF-dependent inhibition of carboxylesterases (Ces), a family of xenobiotic and lipid metabolizing enzymes, whereas AChE activity was inhibited in adult lungs only. Activity-based protein profiling (ABPP)-mass spectrometry of lung microsomes identified 31 and 32 individual serine hydrolases in neonatal lung and adult lung, respectively. Of these, Ces1c/Ces1d/Ces1b isoforms were partially inactivated by CPF in neonatal lung, whereas Ces1c/Ces1b and Ces1c/BChE were partially inactivated in adult female and male lungs, respectively, suggesting age- and sex-related differences in their sensitivity to CPF. Monoacylglycerol lipase (MAGL) and fatty acid amide hydrolase (FAAH) activities in lung were unaffected by CPF. When LPS (1.25 mg/kg, i.p.) was administered following the 7-day CPF dosing period, little to no differences in lung immune responses (cytokines and immunophenotyping) were noted between the CPF and vehicle groups. However, a CPF-dependent increase in the amounts of dendritic cells and certain lipid mediators in female lung following LPS challenge was observed. Experiments in neonatal and adult Ces1d-/- mice yielded similar results as wild type mice (WT) following CPF treatment, except that CPF augmented LPS-induced Tnfa mRNA in adult Ces1d-/- mouse lungs. This effect was associated with decreased expression of Ces1c mRNA in Ces1d-/- mice versus WT mice in the setting of LPS exposure. We conclude that CPF exposure inactivates several Ces isoforms in mouse lung and, during an inflammatory response, increases certain lipid mediators in a female-dependent manner. However, it did not cause widespread altered lung immune effects in response to an LPS challenge.
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Affiliation(s)
- Brittany N Szafran
- Department of Comparative Biomedical Sciences, Center for Environmental Health Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Abdolsamad Borazjani
- Department of Comparative Biomedical Sciences, Center for Environmental Health Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Caitlin N Seay
- Department of Comparative Biomedical Sciences, Center for Environmental Health Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Russell L Carr
- Department of Comparative Biomedical Sciences, Center for Environmental Health Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Richard Lehner
- Departments of Cell Biology and Pediatrics, Group on Molecular & Cell Biology of Lipids, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Barbara L F Kaplan
- Department of Comparative Biomedical Sciences, Center for Environmental Health Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Matthew K Ross
- Department of Comparative Biomedical Sciences, Center for Environmental Health Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi 39762, United States
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Ünsaldı E, Kurt-Kızıldoğan A, Özcan S, Becher D, Voigt B, Aktaş C, Özcengiz G. Proteomic analysis of a hom-disrupted, cephamycin C overproducing Streptomyces clavuligerus. Protein Pept Lett 2021; 28:205-220. [PMID: 32707026 DOI: 10.2174/0929866527666200723163655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 06/18/2020] [Accepted: 06/20/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Streptomyces clavuligerus is prolific producer of cephamycin C, a medically important antibiotic. In our former study, cephamycin C titer was 2-fold improved by disrupting homoserine dehydrogenase (hom) gene of aspartate pahway in Streptomyces clavuligerus NRRL 3585. OBJECTIVE In this article, we aimed to provide a comprehensive understanding at the proteome level on potential complex metabolic changes as a consequence of hom disruption in Streptomyces clavuligerus AK39. METHODS A comparative proteomics study was carried out between the wild type and its hom disrupted AK39 strain by 2 Dimensional Electrophoresis-Matrix Assisted Laser Desorption and Ionization Time-Of-Flight Mass Spectrometry (2DE MALDI-TOF/MS) and Nanoscale Liquid Chromatography- Tandem Mass Spectrometry (nanoLC-MS/MS) analyses. Clusters of Orthologous Groups (COG) database was used to determine the functional categories of the proteins. The theoretical pI and Mw values of the proteins were calculated using Expasy pI/Mw tool. RESULTS "Hypothetical/Unknown" and "Secondary Metabolism" were the most prominent categories of the differentially expressed proteins. Upto 8.7-fold increased level of the positive regulator CcaR was a key finding since CcaR was shown to bind to cefF promoter thereby direcly controlling its expression. Consistently, CeaS2, the first enzyme of CA biosynthetic pathway, was 3.3- fold elevated. There were also many underrepresented proteins associated with the biosynthesis of several Non-Ribosomal Peptide Synthases (NRPSs), clavams, hybrid NRPS/Polyketide synthases (PKSs) and tunicamycin. The most conspicuously underrepresented protein of amino acid metabolism was 4-Hydroxyphenylpyruvate dioxygenase (HppD) acting in tyrosine catabolism. The levels of a Two Component System (TCS) response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain as well as DNA-binding protein HU were elevated while a TetR-family transcriptional regulator was underexpressed. CONCLUSION The results obtained herein will aid in finding out new targets for further improvement of cephamycin C production in Streptomyces clavuligerus.
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Affiliation(s)
- Eser Ünsaldı
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
| | | | - Servet Özcan
- Department of Biology, Erciyes University, Kayseri 38280, Turkey
| | - Dörte Becher
- Institute of Microbiology, Ernst- Moritz-Arndt-University of Greifswald, Greifswald D-17487, Germany
| | - Birgit Voigt
- Institute of Microbiology, Ernst- Moritz-Arndt-University of Greifswald, Greifswald D-17487, Germany
| | - Caner Aktaş
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
| | - Gülay Özcengiz
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
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57
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Decano JL, Singh SA, Gasparotto Bueno C, Ho Lee L, Halu A, Chelvanambi S, Matamalas JT, Zhang H, Mlynarchik AK, Qiao J, Sharma A, Mukai S, Wang J, Anderson DG, Ozaki CK, Libby P, Aikawa E, Aikawa M. Systems Approach to Discovery of Therapeutic Targets for Vein Graft Disease: PPARα Pivotally Regulates Metabolism, Activation, and Heterogeneity of Macrophages and Lesion Development. Circulation 2021; 143:2454-2470. [PMID: 33821665 PMCID: PMC8212880 DOI: 10.1161/circulationaha.119.043724] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Supplemental Digital Content is available in the text. Vein graft failure remains a common clinical challenge. We applied a systems approach in mouse experiments to discover therapeutic targets for vein graft failure.
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Affiliation(s)
- Julius L Decano
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (J.L.D., S.A.S., C.G.B., L.H.L., A.H., S.C., J.T.M., H.Z., A.K.M., J.Q., A.S., S.M., J.W., E.A., M.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Sasha A Singh
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (J.L.D., S.A.S., C.G.B., L.H.L., A.H., S.C., J.T.M., H.Z., A.K.M., J.Q., A.S., S.M., J.W., E.A., M.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Cauê Gasparotto Bueno
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (J.L.D., S.A.S., C.G.B., L.H.L., A.H., S.C., J.T.M., H.Z., A.K.M., J.Q., A.S., S.M., J.W., E.A., M.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Lang Ho Lee
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (J.L.D., S.A.S., C.G.B., L.H.L., A.H., S.C., J.T.M., H.Z., A.K.M., J.Q., A.S., S.M., J.W., E.A., M.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Arda Halu
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (J.L.D., S.A.S., C.G.B., L.H.L., A.H., S.C., J.T.M., H.Z., A.K.M., J.Q., A.S., S.M., J.W., E.A., M.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Channing Division of Network Medicine (A.H., A.S., M.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Sarvesh Chelvanambi
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (J.L.D., S.A.S., C.G.B., L.H.L., A.H., S.C., J.T.M., H.Z., A.K.M., J.Q., A.S., S.M., J.W., E.A., M.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Joan T Matamalas
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (J.L.D., S.A.S., C.G.B., L.H.L., A.H., S.C., J.T.M., H.Z., A.K.M., J.Q., A.S., S.M., J.W., E.A., M.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Hengmin Zhang
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (J.L.D., S.A.S., C.G.B., L.H.L., A.H., S.C., J.T.M., H.Z., A.K.M., J.Q., A.S., S.M., J.W., E.A., M.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Andrew K Mlynarchik
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (J.L.D., S.A.S., C.G.B., L.H.L., A.H., S.C., J.T.M., H.Z., A.K.M., J.Q., A.S., S.M., J.W., E.A., M.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Jiao Qiao
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (J.L.D., S.A.S., C.G.B., L.H.L., A.H., S.C., J.T.M., H.Z., A.K.M., J.Q., A.S., S.M., J.W., E.A., M.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Amitabh Sharma
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (J.L.D., S.A.S., C.G.B., L.H.L., A.H., S.C., J.T.M., H.Z., A.K.M., J.Q., A.S., S.M., J.W., E.A., M.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Channing Division of Network Medicine (A.H., A.S., M.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Shin Mukai
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (J.L.D., S.A.S., C.G.B., L.H.L., A.H., S.C., J.T.M., H.Z., A.K.M., J.Q., A.S., S.M., J.W., E.A., M.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Jianguo Wang
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (J.L.D., S.A.S., C.G.B., L.H.L., A.H., S.C., J.T.M., H.Z., A.K.M., J.Q., A.S., S.M., J.W., E.A., M.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Daniel G Anderson
- Institutes for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge (D.G.A.)
| | - C Keith Ozaki
- Department of Medicine, Division of Vascular and Endovascular Surgery, Department of Surgery (C.K.O.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Peter Libby
- Center for Excellence in Vascular Biology (P.L., E.A., M.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Elena Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (J.L.D., S.A.S., C.G.B., L.H.L., A.H., S.C., J.T.M., H.Z., A.K.M., J.Q., A.S., S.M., J.W., E.A., M.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Center for Excellence in Vascular Biology (P.L., E.A., M.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Department of Human Pathology, I.M. Sechenov First Moscow State Medical University of the Ministry of Health, Russia (E.A., M.A.)
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (J.L.D., S.A.S., C.G.B., L.H.L., A.H., S.C., J.T.M., H.Z., A.K.M., J.Q., A.S., S.M., J.W., E.A., M.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Channing Division of Network Medicine (A.H., A.S., M.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Center for Excellence in Vascular Biology (P.L., E.A., M.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Department of Human Pathology, I.M. Sechenov First Moscow State Medical University of the Ministry of Health, Russia (E.A., M.A.)
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Jia L, Wu J, Wei J, Du L, Wang P, Zhang Y, Yu Y, Wang X, Yang Y, Gao Y. Proteomic analysis of urine reveals biomarkers for the diagnosis and phenotyping of abdominal-type Henoch-Schonlein purpura. Transl Pediatr 2021; 10:510-524. [PMID: 33850810 PMCID: PMC8039785 DOI: 10.21037/tp-20-317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Abdominal-type Henoch-Schonlein purpura (HSP) is a common refractory disease in children. Currently, no specific diagnostic biomarker is available for HSP. METHODS Children with abdominal type HSP were first diagnosed with three syndromes using Chinese traditional medicine. The urinary proteomes among the three syndromes of patients with abdominal type HSP and healthy controls were compared using two label-free proteomics quantifications, including data-dependent acquisition and data-independent acquisition. RESULTS For the comparison between patients with abdominal type HSP and healthy children, a total of 75 differential urinary proteins were identified by determining the overlap of the two experiments. The ingenuity pathway analysis (IPA) analysis showed that these differential proteins were correlated with the pathogenesis of abdominal type HSP. Of these, 37 proteins were distributed in 13 solid tissues as tissue-enriched proteins. Monitoring changes in these proteins might help us detect uncommon clinical manifestations of HSP. Patients with abdominal type HSP can be further distinguished into three syndromes based on the urine proteome. Finally, a panel of six urinary proteins (P25774, P09417, Q7Z5L0, P60900, P14550 and P09668) was constructed for both the diagnosis and phenotyping of abdominal type HSP. CONCLUSIONS Urinary protein biomarkers for the diagnosis and phenotyping of abdominal type HSP were identified, which will contribute to the personalized treatment of patients with abdominal type HSP.
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Affiliation(s)
- Lulu Jia
- Clinical Research Center, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Jianqiang Wu
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jing Wei
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing, China
| | - Lina Du
- Department of Chinese Medicine, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Panpan Wang
- Department of Chinese Medicine, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Yanju Zhang
- Clinical Research Center, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Yuncui Yu
- Clinical Research Center, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Xiaoling Wang
- Clinical Research Center, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Yan Yang
- Department of Chinese Medicine, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Youhe Gao
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing, China
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Gunnarsson S, Prabakaran S. In silico identification of novel open reading frames in Plasmodium falciparum oocyte and salivary gland sporozoites using proteogenomics framework. Malar J 2021; 20:71. [PMID: 33546698 PMCID: PMC7866754 DOI: 10.1186/s12936-021-03598-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/16/2021] [Indexed: 11/25/2022] Open
Abstract
Background Plasmodium falciparum causes the deadliest form of malaria, which remains one of the most prevalent infectious diseases. Unfortunately, the only licensed vaccine showed limited protection and resistance to anti-malarial drug is increasing, which can be largely attributed to the biological complexity of the parasite’s life cycle. The progression from one developmental stage to another in P. falciparum involves drastic changes in gene expressions, where its infectivity to human hosts varies greatly depending on the stage. Approaches to identify candidate genes that are responsible for the development of infectivity to human hosts typically involve differential gene expression analysis between stages. However, the detection may be limited to annotated proteins and open reading frames (ORFs) predicted using restrictive criteria. Methods The above problem is particularly relevant for P. falciparum; whose genome annotation is relatively incomplete given its clinical significance. In this work, systems proteogenomics approach was used to address this challenge, as it allows computational detection of unannotated, novel Open Reading Frames (nORFs), which are neglected by conventional analyses. Two pairs of transcriptome/proteome were obtained from a previous study where one was collected in the mosquito-infectious oocyst sporozoite stage, and the other in the salivary gland sporozoite stage with human infectivity. They were then re-analysed using the proteogenomics framework to identify nORFs in each stage. Results Translational products of nORFs that map to antisense, intergenic, intronic, 3′ UTR and 5′ UTR regions, as well as alternative reading frames of canonical proteins were detected. Some of these nORFs also showed differential expression between the two life cycle stages studied. Their regulatory roles were explored through further bioinformatics analyses including the expression regulation on the parent reference genes, in silico structure prediction, and gene ontology term enrichment analysis. Conclusion The identification of nORFs in P. falciparum sporozoites highlights the biological complexity of the parasite. Although the analyses are solely computational, these results provide a starting point for further experimental validation of the existence and functional roles of these nORFs,
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Affiliation(s)
- Sophie Gunnarsson
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Sudhakaran Prabakaran
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK.
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Dahlgren KK, Gates C, Lee T, Cameron JC. Proximity-based proteomics reveals the thylakoid lumen proteome in the cyanobacterium Synechococcus sp. PCC 7002. PHOTOSYNTHESIS RESEARCH 2021; 147:177-195. [PMID: 33280076 PMCID: PMC7880944 DOI: 10.1007/s11120-020-00806-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Cyanobacteria possess unique intracellular organization. Many proteomic studies have examined different features of cyanobacteria to learn about the intracellular structures and their respective functions. While these studies have made great progress in understanding cyanobacterial physiology, the conventional fractionation methods used to purify cellular structures have limitations; specifically, certain regions of cells cannot be purified with existing fractionation methods. Proximity-based proteomics techniques were developed to overcome the limitations of biochemical fractionation for proteomics. Proximity-based proteomics relies on spatiotemporal protein labeling followed by mass spectrometry of the labeled proteins to determine the proteome of the region of interest. We performed proximity-based proteomics in the cyanobacterium Synechococcus sp. PCC 7002 with the APEX2 enzyme, an engineered ascorbate peroxidase. We determined the proteome of the thylakoid lumen, a region of the cell that has remained challenging to study with existing methods, using a translational fusion between APEX2 and PsbU, a lumenal subunit of photosystem II. Our results demonstrate the power of APEX2 as a tool to study the cell biology of intracellular features and processes, including photosystem II assembly in cyanobacteria, with enhanced spatiotemporal resolution.
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Affiliation(s)
- Kelsey K Dahlgren
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, 80309, USA
- Interdisciplinary Quantitative Biology Program (IQ Biology), BioFrontiers Institute, University of Colorado, Boulder, CO, 80309, USA
| | - Colin Gates
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA
| | - Thomas Lee
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
| | - Jeffrey C Cameron
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA.
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA.
- National Renewable Energy Laboratory, Golden, CO, 80401, USA.
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Yamada K, Nishimura T, Wakiya M, Satoh E, Fukuda T, Amaya K, Bando Y, Hirano H, Ishikawa T. Protein co-expression networks identified from HOT lesions of ER+HER2-Ki-67high luminal breast carcinomas. Sci Rep 2021; 11:1705. [PMID: 33462336 PMCID: PMC7814020 DOI: 10.1038/s41598-021-81509-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/05/2021] [Indexed: 01/20/2023] Open
Abstract
Patients with estrogen receptor-positive/human epidermal growth factor receptor 2-negative/Ki-67-high (ER+HER2-Ki-67high) luminal breast cancer have a worse prognosis and do not respond to hormonal treatment and chemotherapy. This study sought to identify disease-related protein networks significantly associated with this subtype, by assessing in-depth proteomes of 10 lesions of high and low Ki-67 values (HOT, five; COLD, five) microdissected from the five tumors. Weighted correlation network analysis screened by over-representative analysis identified the five modules significantly associated with the HOT lesions. Pathway enrichment analysis, together with causal network analysis, revealed pathways of ribosome-associated quality controls, heat shock response by oxidative stress and hypoxia, angiogenesis, and oxidative phosphorylation. A semi-quantitative correlation of key-protein expressions, protein co-regulation analysis, and multivariate correlation analysis suggested co-regulations via network-network interaction among the four HOT-characteristic modules. Predicted highly activated master and upstream regulators were most characteristic to ER-positive breast cancer and associated with oncogenic transformation, as well as resistance to chemotherapy and endocrine therapy. Interestingly, inhibited intervention causal networks of numerous chemical inhibitors were predicted within the top 10 lists for the WM2 and WM5 modules, suggesting involvement of potential therapeutic targets in those data-driven networks. Our findings may help develop therapeutic strategies to benefit patients.
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Affiliation(s)
- Kimito Yamada
- Department of Breast Surgery, Tokyo Medical University Hachioji Medical Centre, Tokyo, 193-0998, Japan
- Department of Breast Surgery, Tokyo Medical University Hospital, Tokyo, 160-0023, Japan
| | - Toshihide Nishimura
- Department of Translational Medicine Informatics, St. Marianna University School of Medicine, Kanagawa, 216-8511, Japan.
| | - Midori Wakiya
- Department of Diagnostic Pathology, Tokyo Medical University Hachioji Medical Centre, Tokyo, 193-0998, Japan
| | - Eiichi Satoh
- Department of Pathology, Institute of Medical Science, Tokyo Medical University, Tokyo, 160-0023, Japan
| | - Tetsuya Fukuda
- Research and Development, Biosys Technologies Inc, Tokyo, 152-0031, Japan
| | - Keigo Amaya
- Department of Breast Surgery, Tokyo Medical University Hachioji Medical Centre, Tokyo, 193-0998, Japan
| | - Yasuhiko Bando
- Research and Development, Biosys Technologies Inc, Tokyo, 152-0031, Japan
| | - Hiroshi Hirano
- Department of Diagnostic Pathology, Tokyo Medical University Hachioji Medical Centre, Tokyo, 193-0998, Japan
| | - Takashi Ishikawa
- Department of Breast Surgery, Tokyo Medical University Hospital, Tokyo, 160-0023, Japan
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Gatti M, Beretti F, Zavatti M, Bertucci E, Ribeiro Luz S, Palumbo C, Maraldi T. Amniotic Fluid Stem Cell-Derived Extracellular Vesicles Counteract Steroid-Induced Osteoporosis In Vitro. Int J Mol Sci 2020; 22:ijms22010038. [PMID: 33375177 PMCID: PMC7792960 DOI: 10.3390/ijms22010038] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 12/19/2022] Open
Abstract
Background—Osteoporosis is characterized by defects in both quality and quantity of bone tissue, which imply high susceptibility to fractures with limitations of autonomy. Current therapies for osteoporosis are mostly concentrated on how to inhibit bone resorption but give serious adverse effects. Therefore, more effective and safer therapies are needed that even encourage bone formation. Here we examined the effect of extracellular vesicles secreted by human amniotic fluid stem cells (AFSC) (AFSC-EV) on a model of osteoporosis in vitro. Methods—human AFSC-EV were added to the culture medium of a human pre-osteoblast cell line (HOB) induced to differentiate, and then treated with dexamethasone as osteoporosis inducer. Aspects of differentiation and viability were assessed by immunofluorescence, Western blot, mass spectrometry, and histological assays. Since steroids induce oxidative stress, the levels of reactive oxygen species and of redox related proteins were evaluated. Results—AFSC-EV were able to ameliorate the differentiation ability of HOB both in the case of pre-osteoblasts and when the differentiation process was affected by dexamethasone. Moreover, the viability was increased and parallelly apoptotic markers were reduced. The presence of EV positively modulated the redox unbalance due to dexamethasone. Conclusion—these findings demonstrated that EV from hAFSC have the ability to recover precursor cell potential and delay local bone loss in steroid-related osteoporosis.
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Affiliation(s)
- Martina Gatti
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (M.G.); (F.B.); (M.Z.); (S.R.L.); (C.P.)
| | - Francesca Beretti
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (M.G.); (F.B.); (M.Z.); (S.R.L.); (C.P.)
| | - Manuela Zavatti
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (M.G.); (F.B.); (M.Z.); (S.R.L.); (C.P.)
| | - Emma Bertucci
- Department of Medical and Surgical Sciences for Mothers, Children and Adults, University of Modena and Reggio Emilia, Azienda Ospedaliero Universitaria Policlinico, Via Del Pozzo 71, 41124 Modena, Italy;
| | - Soraia Ribeiro Luz
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (M.G.); (F.B.); (M.Z.); (S.R.L.); (C.P.)
| | - Carla Palumbo
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (M.G.); (F.B.); (M.Z.); (S.R.L.); (C.P.)
| | - Tullia Maraldi
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (M.G.); (F.B.); (M.Z.); (S.R.L.); (C.P.)
- Correspondence: ; Tel.: +39-05-9422-3178; Fax: +39-05-9422-4859
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Proteomic profiles and cytokeratin 13 as a potential biomarker of Ovis aries papillomavirus 3-positive and negative cutaneous squamous cell carcinomas. Res Vet Sci 2020; 134:112-119. [PMID: 33360571 DOI: 10.1016/j.rvsc.2020.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 10/22/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022]
Abstract
Ovis aries papillomavirus 3 (OaPV3) is an epidermotropic PV reported in sheep cutaneous squamous cell carcinoma (SCC). The presence of OaPV3 DNA and its transcriptional activity in cutaneous SCC, as well as its in vitro transforming properties, suggest a viral etiology for this neoplasm. Nevertheless, the reactome associated with viral-host interaction is still unexplored. Here, we investigated and compared the proteomic profiles of OaPV3-positive SCCs, OaPV3-negative SCCs, and non-SCC samples by liquid chromatography tandem-mass spectrometry (LC-MS/MS) analysis, bioinformatics tools, and immunohistochemistry (IHC). OaPV3-positive SCCs (n = 3), OaPV3-negative SCCs (n = 3), and non-SCCs samples (n = 3) were subjected to a shotgun proteomic analysis workflow to assess protein abundance differences among the three sample classes. Proteins involved in epithelial cell differentiation, extracellular matrix organization, and apoptotic signaling showed different abundances in OaPV3-positive SCCs tissues (P ≤ 0.05) when compared to the other tissues. Cytokeratin 13 (CK 13) was among the most increased proteins in OaPV3-positive SCC and was validated by immunohistochemistry on 10 samples per class, confirming its potential as a biomarker of OaPV3 infection in SCC. Collectively, results provide a preliminary insight into the reactome associated with viral-host interaction and pave the way to the development of specific biomarkers for viral-induced sheep SCC.
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Arrant AE, Davis SE, Vollmer RM, Murchison CF, Mobley JA, Nana AL, Spina S, Grinberg LT, Karydas AM, Miller BL, Seeley WW, Roberson ED. Elevated levels of extracellular vesicles in progranulin-deficient mice and FTD-GRN Patients. Ann Clin Transl Neurol 2020; 7:2433-2449. [PMID: 33197149 PMCID: PMC7732244 DOI: 10.1002/acn3.51242] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/22/2020] [Accepted: 10/18/2020] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE The goal of this study was to investigate the effect of progranulin insufficiency on extracellular vesicles (EVs), a heterogeneous population of vesicles that may contribute to progression of neurodegenerative disease. Loss-of-function mutations in progranulin (GRN) are a major cause of frontotemporal dementia (FTD), and brains from GRN carriers with FTD (FTD-GRN) exhibit signs of lysosomal dysfunction. Lysosomal dysfunction may induce compensatory increases in secretion of exosomes, EVs secreted from the endolysosomal system, so we hypothesized that progranulin insufficiency would increase EV levels in the brain. METHODS We analyzed levels and protein contents of brain EVs from Grn-/- mice, which model the lysosomal abnormalities of FTD-GRN patients. We then measured brain EVs in FTD-GRN patients. To assess the relationship of EVs with symptomatic disease, we measured plasma EVs in presymptomatic and symptomatic GRN mutation carriers. RESULTS Grn-/- mice had elevated brain EV levels and altered EV protein contents relative to wild-type mice. These changes were age-dependent, occurring only after the emergence of pathology in Grn-/- mice. FTD-GRN patients (n = 13) had elevated brain EV levels relative to controls (n = 5). Symptomatic (n = 12), but not presymptomatic (n = 7), GRN carriers had elevated plasma EV levels relative to controls (n = 8). INTERPRETATION These data show that symptomatic FTD-GRN patients have elevated levels of brain and plasma EVs, and that this effect is modeled in the brain of Grn-/- mice after the onset of pathology. This increase in EVs could influence FTD disease progression, and provides further support for EVs as potential FTD biomarkers.
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Affiliation(s)
- Andrew E. Arrant
- Departments of Neurology and NeurobiologyCenter for Neurodegeneration and Experimental TherapeuticsAlzheimer’s Disease CenterEvelyn F. McKnight Brain InstituteUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Skylar E. Davis
- Departments of Neurology and NeurobiologyCenter for Neurodegeneration and Experimental TherapeuticsAlzheimer’s Disease CenterEvelyn F. McKnight Brain InstituteUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Rachael M. Vollmer
- Departments of Neurology and NeurobiologyCenter for Neurodegeneration and Experimental TherapeuticsAlzheimer’s Disease CenterEvelyn F. McKnight Brain InstituteUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Charles F. Murchison
- Departments of Neurology and NeurobiologyCenter for Neurodegeneration and Experimental TherapeuticsAlzheimer’s Disease CenterEvelyn F. McKnight Brain InstituteUniversity of Alabama at BirminghamBirminghamAlabamaUSA
- Department of BiostatisticsUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - James A. Mobley
- Department of SurgeryUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Alissa L. Nana
- Department of NeurologyMemory and Aging CenterUCSF Weill Institute for NeurosciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Salvatore Spina
- Department of NeurologyMemory and Aging CenterUCSF Weill Institute for NeurosciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Lea T. Grinberg
- Department of NeurologyMemory and Aging CenterUCSF Weill Institute for NeurosciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
- Department of PathologyUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Anna M. Karydas
- Department of NeurologyMemory and Aging CenterUCSF Weill Institute for NeurosciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Bruce L. Miller
- Department of NeurologyMemory and Aging CenterUCSF Weill Institute for NeurosciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - William W. Seeley
- Department of NeurologyMemory and Aging CenterUCSF Weill Institute for NeurosciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
- Department of PathologyUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Erik D. Roberson
- Departments of Neurology and NeurobiologyCenter for Neurodegeneration and Experimental TherapeuticsAlzheimer’s Disease CenterEvelyn F. McKnight Brain InstituteUniversity of Alabama at BirminghamBirminghamAlabamaUSA
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Tian J, Du J, Han J, Bao X, Song X, Lu Z. Proteomics reveals the preliminary physiological states of the spotted seal (Phoca largha) pups. Sci Rep 2020; 10:18727. [PMID: 33127980 PMCID: PMC7599241 DOI: 10.1038/s41598-020-75759-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 10/20/2020] [Indexed: 02/07/2023] Open
Abstract
Spotted seal (Phoca largha) is a critically endangered pinniped in China and South Korea. The conventional method to protect and maintain the P. largha population is to keep them captive in artificially controlled environments. However, little is known about the physiological differences between wild and captive P. largha. To generate a preliminary protein expression profile for P. largha, whole blood from wild and captive pups were subjected to a label-free comparative proteomic analysis. According to the results, 972 proteins were identified and predicted to perform functions related to various metabolic, immune, and cellular processes. Among the identified proteins, the expression level of 51 were significantly different between wild and captive P. large pups. These differentially expressed proteins were enriched in a wide range of cellular functions, including cytoskeleton, phagocytosis, proteolysis, the regulation of gene expression, and carbohydrate metabolism. The abundances of proteins involved in phagocytosis and ubiquitin-mediated proteolysis were significantly higher in the whole blood of wild P. largha pups than in captive individuals. In addition, heat shock protein 90-beta, were determined as the key protein associated with the differences in the wild and captive P. largha pups due to the most interactions of it with various differentially expressed proteins. Moreover, wild P. largha pups could be more nutritionally stressed and have more powerful immune capacities than captive pups. This study provides the first data on the protein composition of P. largha and provides useful information on the physiological characteristics for research in this species.
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Affiliation(s)
- Jiashen Tian
- Dalian Key Laboratory of Conservation Biology for Endangered Marine Mammals, Liaoning Ocean and Fisheries Science Research Institute, 50 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Jing Du
- Dalian Key Laboratory of Conservation Biology for Endangered Marine Mammals, Liaoning Ocean and Fisheries Science Research Institute, 50 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Jiabo Han
- Dalian Key Laboratory of Conservation Biology for Endangered Marine Mammals, Liaoning Ocean and Fisheries Science Research Institute, 50 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Xiangbo Bao
- Dalian Key Laboratory of Conservation Biology for Endangered Marine Mammals, Liaoning Ocean and Fisheries Science Research Institute, 50 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Xinran Song
- Dalian Sun Asia Tourism Holding Co., Ltd., 608-6-8 Zhongshan Road, Shahekou District, Dalian, 116023, China
| | - Zhichuang Lu
- Dalian Key Laboratory of Conservation Biology for Endangered Marine Mammals, Liaoning Ocean and Fisheries Science Research Institute, 50 Heishijiao Street, Shahekou District, Dalian, 116023, China.
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Truong T, Pang LM, Rajan S, Wong SSW, Fung YME, Samaranayake L, Seneviratne CJ. The Proteome of Community Living Candida albicans Is Differentially Modulated by the Morphologic and Structural Features of the Bacterial Cohabitants. Microorganisms 2020; 8:microorganisms8101541. [PMID: 33036329 PMCID: PMC7601143 DOI: 10.3390/microorganisms8101541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/02/2020] [Accepted: 10/03/2020] [Indexed: 11/16/2022] Open
Abstract
Candida albicans is a commensal polymorphic and opportunistic fungus, which usually resides as a small community in the oral cavities of a majority of humans. The latter eco-system presents this yeast varied opportunities for mutualistic interactions with other cohabitant oral bacteria, that synergizes its persistence and pathogenicity. Collectively, these communities live within complex plaque biofilms which may adversely affect the oral health and increase the proclivity for oral candidiasis. The proteome of such oral biofilms with myriad interkingdom interactions are largely underexplored. Herein, we employed limma differential expression analysis, and cluster analysis to explore the proteomic interactions of C. albicans biofilms with nine different common oral bacterial species, Aggregatibacter actinomycetemcomitans, Actinomyces naeslundii, Fusobacterium nucleatum, Enterococcus faecalis, Porphyromonas gingivalis, Streptococcus mutants, Streptococcus sanguinis, Streptococcus mitis, and Streptococcus sobrinus. Interestingly, upon exposure of C. albicans biofilms to the foregoing heat-killed bacteria, the proteomes of the fungus associated with cellular respiration, translation, oxidoreductase activity, and ligase activity were significantly altered. Subsequent differential expression and cluster analysis revealed the subtle, yet significant alterations in the C. albicans proteome, particularly on exposure to bacteria with dissimilar cell morphologies, and Gram staining characteristics.
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Affiliation(s)
- Thuyen Truong
- Oral Sciences, Faculty of Dentistry, National University of Singapore, Singapore 119085, Singapore;
| | - Li Mei Pang
- National Dental Research Institute Singapore (NDRIS), National Dental Centre Singapore, Singapore 168938, Singapore;
| | - Suhasini Rajan
- Walther Straub Institute of Pharmacology and Toxicology, Member of the German Center for Lung Research (DZL), Medical Faculty, LMU-Munich, 80336 Munich, Germany;
| | - Sarah Sze Wah Wong
- Molecular Mycology Unit, Institut Pasteur, CNRS, UMR2000, 10098 Paris, France;
| | - Yi Man Eva Fung
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China;
| | - Lakshman Samaranayake
- College of Dental Medicine, University of Sharjah, Sharjah 27272, UAE;
- Faculty of Dentistry, The University of Hong Kong, Hong Kong, China
| | - Chaminda Jayampath Seneviratne
- National Dental Research Institute Singapore (NDRIS), National Dental Centre Singapore, Singapore 168938, Singapore;
- Oral Health Academic Clinical Programme, Duke-NUS Medical School, Singapore 169857, Singapore
- Correspondence: ; Tel.: +65-65767141
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Cozzolino F, Landolfi A, Iacobucci I, Monaco V, Caterino M, Celentano S, Zuccato C, Cattaneo E, Monti M. New label-free methods for protein relative quantification applied to the investigation of an animal model of Huntington Disease. PLoS One 2020; 15:e0238037. [PMID: 32886703 PMCID: PMC7473538 DOI: 10.1371/journal.pone.0238037] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/07/2020] [Indexed: 12/27/2022] Open
Abstract
Spectral Counts approaches (SpCs) are largely employed for the comparison of protein expression profiles in label-free (LF) differential proteomics applications. Similarly, to other comparative methods, also SpCs based approaches require a normalization procedure before Fold Changes (FC) calculation. Here, we propose new Complexity Based Normalization (CBN) methods that introduced a variable adjustment factor (f), related to the complexity of the sample, both in terms of total number of identified proteins (CBN(P)) and as total number of spectral counts (CBN(S)). Both these new methods were compared with the Normalized Spectral Abundance Factor (NSAF) and the Spectral Counts log Ratio (Rsc), by using standard protein mixtures. Finally, to test the robustness and the effectiveness of the CBNs methods, they were employed for the comparative analysis of cortical protein extract from zQ175 mouse brains, model of Huntington Disease (HD), and control animals (raw data available via ProteomeXchange with identifier PXD017471). LF data were also validated by western blot and MRM based experiments. On standard mixtures, both CBN methods showed an excellent behavior in terms of reproducibility and coefficients of variation (CVs) in comparison to the other SpCs approaches. Overall, the CBN(P) method was demonstrated to be the most reliable and sensitive in detecting small differences in protein amounts when applied to biological samples.
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Affiliation(s)
- Flora Cozzolino
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy
- CEINGE Advanced Biotechnologies, Naples, Italy
| | - Alfredo Landolfi
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy
- CEINGE Advanced Biotechnologies, Naples, Italy
| | - Ilaria Iacobucci
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy
- CEINGE Advanced Biotechnologies, Naples, Italy
| | | | - Marianna Caterino
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Naples, Italy
| | | | - Chiara Zuccato
- Department of Biosciences, University of Milan, Milan, Italy
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Elena Cattaneo
- Department of Biosciences, University of Milan, Milan, Italy
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Maria Monti
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy
- CEINGE Advanced Biotechnologies, Naples, Italy
- * E-mail:
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Guerreiro EM, Øvstebø R, Thiede B, Costea DE, Søland TM, Kanli Galtung H. Cancer cell line-specific protein profiles in extracellular vesicles identified by proteomics. PLoS One 2020; 15:e0238591. [PMID: 32886718 PMCID: PMC7473518 DOI: 10.1371/journal.pone.0238591] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/19/2020] [Indexed: 12/15/2022] Open
Abstract
Extracellular vesicles (EVs), are important for intercellular communication in both physiological and pathological processes. To explore the potential of cancer derived EVs as disease biomarkers for diagnosis, monitoring, and treatment decision, it is necessary to thoroughly characterize their biomolecular content. The aim of the study was to characterize and compare the protein content of EVs derived from three different cancer cell lines in search of a specific molecular signature, with emphasis on proteins related to the carcinogenic process. Oral squamous cell carcinoma (OSCC), pancreatic ductal adenocarcinoma (PDAC) and melanoma brain metastasis cell lines were cultured in CELLine AD1000 flasks. EVs were isolated by ultrafiltration and size-exclusion chromatography and characterized. Next, the isolated EVs underwent liquid chromatography-mass spectrometry (LC-MS) analysis for protein identification. Functional enrichment analysis was performed for a more general overview of the biological processes involved. More than 600 different proteins were identified in EVs from each particular cell line. Here, 14%, 10%, and 24% of the identified proteins were unique in OSCC, PDAC, and melanoma vesicles, respectively. A specific protein profile was discovered for each cell line, e.g., EGFR in OSCC, Muc5AC in PDAC, and FN1 in melanoma vesicles. Nevertheless, 25% of all the identified proteins were common to all cell lines. Functional enrichment analysis linked the proteins in each data set to biological processes such as "biological adhesion", "cell motility", and "cellular component biogenesis". EV proteomics discovered cancer-specific protein profiles, with proteins involved in processes promoting tumor progression. In addition, the biological processes associated to the melanoma-derived EVs were distinct from the ones linked to the EVs isolated from OSCC and PDAC. The malignancy specific biomolecular cues in EVs may have potential applications as diagnostic biomarkers and in therapy.
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Affiliation(s)
- Eduarda M. Guerreiro
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Reidun Øvstebø
- Department of Medical Biochemistry, Blood Cell Research Group, Oslo University Hospital, Ullevål, Oslo, Norway
| | - Bernd Thiede
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Daniela Elena Costea
- Centre for Cancer Biomarkers CCBio and Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Tine M. Søland
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Hilde Kanli Galtung
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
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69
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Nishimura T, Végvári Á, Nakamura H, Kato H, Saji H. Mutant Proteomics of Lung Adenocarcinomas Harboring Different EGFR Mutations. Front Oncol 2020; 10:1494. [PMID: 32983988 PMCID: PMC7477350 DOI: 10.3389/fonc.2020.01494] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/13/2020] [Indexed: 12/28/2022] Open
Abstract
Epidermal growth factor receptor EGFR major driver mutations may affect downstream molecular networks and pathways, which would influence treatment outcomes of non-small cell lung cancer (NSCLC). This study aimed to unveil profiles of mutant proteins expressed in lung adenocarcinomas of 36 patients harboring representative driver EGFR mutations (Ex19del, nine; L858R, nine; no Ex19del/L858R, 18). Surprisingly, the orthogonal partial least squares discriminant analysis performed for identified mutant proteins demonstrated the profound differences in distance among the different EGFR mutation groups, suggesting that cancer cells harboring L858R or Ex19del emerge from cellular origins different from L858R/Ex19del-negative cells. Weighted gene coexpression network analysis, together with over-representative analysis, identified 18 coexpressed modules and their eigen proteins. Pathways enriched differentially for both the L858R and Ex19del mutations included carboxylic acid metabolic process, cell cycle, developmental biology, cellular responses to stress, mitotic prophase, cell proliferation, growth, epithelial to mesenchymal transition (EMT), and immune system. The IPA causal network analysis identified the highly activated networks of PARPBP, HOXA1, and APH1 under the L858R mutation, whereas those of ASGR1, APEX1, BUB1, and MAPK10 were highly activated under the Ex19del mutation. Interestingly, the downregulated causal network of osimertinib intervention showed the highest significance in overlap p-value among most causal networks predicted under the L858R mutation. We also identified the causal network of MAPK interacting serine/threonine kinase 1/2 (MNK1/2) highly activated differentially under the L858R mutation. Tumor-suppressor AMOT, a component of the Hippo pathways, was highly inhibited commonly under both L858R and Ex19del mutations. Our results could identify disease-related protein molecular networks from the landscape of single amino acid variants. Our findings may help identify potential therapeutic targets and develop therapeutic strategies to improve patient outcomes.
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Affiliation(s)
- Toshihide Nishimura
- Department of Translational Medicine Informatics, St. Marianna University School of Medicine, Kawasaki, Japan
- Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Ákos Végvári
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Haruhiko Nakamura
- Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Harubumi Kato
- Division of Thoracic and Thyroid Surgery, Tokyo Medical University, Tokyo, Japan
- Research Institute of Health and Welfare Sciences, Graduate School, International University of Health and Welfare, Tokyo, Japan
| | - Hisashi Saji
- Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
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70
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PeptideWitch-A Software Package to Produce High-Stringency Proteomics Data Visualizations from Label-Free Shotgun Proteomics Data. Proteomes 2020; 8:proteomes8030021. [PMID: 32825686 PMCID: PMC7564585 DOI: 10.3390/proteomes8030021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/13/2020] [Accepted: 08/18/2020] [Indexed: 12/18/2022] Open
Abstract
PeptideWitch is a python-based web module that introduces several key graphical and technical improvements to the Scrappy software platform, which is designed for label-free quantitative shotgun proteomics analysis using normalised spectral abundance factors. The program inputs are low stringency protein identification lists output from peptide-to-spectrum matching search engines for ‘control’ and ‘treated’ samples. Through a combination of spectral count summation and inner joins, PeptideWitch processes low stringency data, and outputs high stringency data that are suitable for downstream quantitation. Data quality metrics are generated, and a series of statistical analyses and graphical representations are presented, aimed at defining and presenting the difference between the two sample proteomes.
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71
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VCP Machinery Mediates Autophagic Degradation of Empty Argonaute. Cell Rep 2020; 28:1144-1153.e4. [PMID: 31365860 DOI: 10.1016/j.celrep.2019.07.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/12/2019] [Accepted: 06/27/2019] [Indexed: 12/29/2022] Open
Abstract
The Argonaute subfamily of proteins (AGO) loads microRNAs (miRNAs) to form the effector complex that mediates target gene silencing. Empty AGO, but not miRNA-loaded AGO, is selectively degraded across species. We have reported that the degradation of empty AGO is part of a quality control pathway that eliminates dysfunctional AGO. However, how empty AGO is degraded remains unclear. Here we show that the empty state of Drosophila Ago1 is degraded by autophagy. Comprehensive LC-MS/MS analyses, together with manipulation of the Ago1 ubiquitination level, revealed that VCP, which mediates selective autophagy, recognizes empty Ago1 via the Ufd1-Npl4 heterodimer. Depletion of VCP-Ufd1-Npl4 machinery impairs degradation of empty Ago1 and miRNA-mediated target gene silencing. Our findings reveal a direct link between empty AGO degradation and selective autophagy that ensures efficient miRNA function.
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72
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Folkesson E, Turkiewicz A, Ali N, Rydén M, Hughes H, Tjörnstrand J, Önnerfjord P, Englund M. Proteomic comparison of osteoarthritic and reference human menisci using data-independent acquisition mass spectrometry. Osteoarthritis Cartilage 2020; 28:1092-1101. [PMID: 32407894 PMCID: PMC7397514 DOI: 10.1016/j.joca.2020.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/09/2020] [Accepted: 05/01/2020] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Recent research in knee osteoarthritis (OA) highlights the role of the meniscus in OA pathology. Our aim was to compare the proteomes of medial and lateral menisci from end-stage medial compartment knee OA patients, with reference menisci from knee-healthy deceased donors, using mass spectrometry. DESIGN Tissue plugs of Ø3 mm were obtained from the posterior horns of the lateral and medial menisci from one knee of 10 knee-healthy deceased donors and 10 patients undergoing knee replacement. Proteins were extracted and prepared for mass spectrometric analysis. Statistical analysis was conducted on abundance data that was log2-transformed, using a linear mixed effects model and evaluated using pathway analysis. RESULTS We identified a total of 835 proteins in all samples, of which 331 were included in the statistical analysis. The largest differences could be seen between the medial menisci from OA patients and references, with most proteins showing higher intensities in the medial menisci from OA patients. Several matrix proteins, e.g., matrix metalloproteinase 3 (MMP3) (4.3 times higher values [95%CI 1.8, 10.6]), TIMP1 (3.5 [1.4, 8.5]), asporin (4.1 [1.7, 10.0]) and versican (4.4 [1.8, 10.9]), all showed higher abundance in medial menisci from OA patients compared to medial reference menisci. OA medial menisci also showed increased activation of several pathways involved in inflammation. CONCLUSION An increase in protein abundance for proteins such as MMP and TIMP1 in the medial menisci from OA patients suggests simultaneous activation of both catabolic and anabolic processes that warrants further attention.
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Affiliation(s)
- E. Folkesson
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Orthopaedics, Clinical Epidemiology Unit, Lund, Sweden,Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Rheumatology and Molecular Skeletal Biology, Lund, Sweden,Address correspondence and reprint requests to: E. Folkesson, Department of Clinical Sciences Lund, Lund University Molecular Skeletal Biology - BMC-C12, Klinikgatan 28, 221 00, Lund, Sweden.
| | - A. Turkiewicz
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Orthopaedics, Clinical Epidemiology Unit, Lund, Sweden
| | - N. Ali
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Orthopaedics, Clinical Epidemiology Unit, Lund, Sweden
| | - M. Rydén
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Orthopaedics, Clinical Epidemiology Unit, Lund, Sweden
| | - H.V. Hughes
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Orthopaedics, Clinical Epidemiology Unit, Lund, Sweden
| | - J. Tjörnstrand
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Orthopaedics, Clinical Epidemiology Unit, Lund, Sweden,Department of Orthopaedics, Skåne University Hospital, Lund, Sweden
| | - P. Önnerfjord
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Rheumatology and Molecular Skeletal Biology, Lund, Sweden
| | - M. Englund
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Orthopaedics, Clinical Epidemiology Unit, Lund, Sweden,Clinical Epidemiology Research and Training Unit, Boston University School of Medicine, Boston, MA, USA
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73
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Addis DR, Aggarwal S, Doran SF, Jian MY, Ahmad I, Kojima K, Ford DA, Matalon S, Mobley JA. Vascular permeability disruption explored in the proteomes of mouse lungs and human microvascular cells following acute bromine exposure. Am J Physiol Lung Cell Mol Physiol 2020; 319:L337-L359. [PMID: 32579402 PMCID: PMC7473936 DOI: 10.1152/ajplung.00196.2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 01/22/2023] Open
Abstract
Bromine (Br2) is an organohalide found in nature and is integral to many manufacturing processes. Br2 is toxic to living organisms, and high concentrations can prove fatal. To meet industrial demand, large amounts of purified Br2 are produced, transported, and stored worldwide, providing a multitude of interfaces for potential human exposure through either accidents or terrorism. To identify the key mechanisms associated with acute Br2 exposure, we have surveyed the lung proteomes of C57BL/6 male mice and human lung-derived microvascular endothelial cells (HMECs) at 24 h following exposure to Br2 in concentrations likely to be encountered in the vicinity of industrial accidents. Global discovery proteomics applications combined with systems biology analysis identified robust and highly significant changes in proteins associated with three biological processes: 1) exosome secretion, 2) inflammation, and 3) vascular permeability. We focused on the latter, conducting physiological studies on isolated perfused lungs harvested from mice 24 h after Br2 exposure. These experiments revealed significant increases in the filtration coefficient (Kf) indicating increased permeability of the pulmonary vasculature. Similarly, confluent monolayers of Br2 and Br-lipid-treated HMECs exhibited differential levels of zona occludens-1 that were found to be dissociated from cell wall localization, an increase in phosphorylation and internalization of E-cadherin, as well as increased actin stress fiber formation, all of which are consistent with increased permeability. Taken as a whole, our discovery proteomics and systems analysis workflow, combined with physiological measurements of permeability, revealed both profound and novel biological changes that contribute to our current understanding of Br2 toxicity.
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Affiliation(s)
- Dylan R Addis
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
- Pulmonary Injury and Repair Center, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
- Division of Cardiothoracic Anesthesiology, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Saurabh Aggarwal
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
- Pulmonary Injury and Repair Center, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Stephen F Doran
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
- Pulmonary Injury and Repair Center, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Ming-Yuan Jian
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
- Pulmonary Injury and Repair Center, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Israr Ahmad
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
- Pulmonary Injury and Repair Center, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Kyoko Kojima
- Comprehensive Cancer Center, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - David A Ford
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri
| | - Sadis Matalon
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
- Pulmonary Injury and Repair Center, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - James A Mobley
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
- Pulmonary Injury and Repair Center, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
- Comprehensive Cancer Center, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
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74
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Folkesson E, Turkiewicz A, Rydén M, Hughes HV, Ali N, Tjörnstrand J, Önnerfjord P, Englund M. Proteomic characterization of the normal human medial meniscus body using data-independent acquisition mass spectrometry. J Orthop Res 2020; 38:1735-1745. [PMID: 31989678 PMCID: PMC7610686 DOI: 10.1002/jor.24602] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 01/02/2020] [Accepted: 01/21/2020] [Indexed: 02/04/2023]
Abstract
Recent research suggests an important role of the meniscus in the development of knee osteoarthritis. We, therefore, aimed to analyze the proteome of the normal human meniscus body, and specifically to gain new knowledge on global protein expression in the different radial zones. Medial menisci were retrieved from the right knees of 10 human cadaveric donors, from which we cut a 2 mm radial slice from the mid-portion of the meniscal body. This slice was further divided into three zones: inner, middle, and peripheral. Proteins were extracted and prepared for mass spectrometric analysis using data-independent acquisition. We performed subsequent data searches using Spectronaut Pulsar and used fixed-effect linear regression models for statistical analysis. We identified 638 proteins and after statistical analysis, we observed the greatest number of differentially expressed proteins between the inner and peripheral zones (163 proteins) and the peripheral and middle zones (136 proteins), with myocilin being the protein with the largest fold-change in both comparisons. Chondroadherin was one of eight proteins that differed between the inner and middle zones. Functional enrichment analyses showed that the peripheral one-third of the medial meniscus body differed substantially from the two more centrally located zones, which were more similar to each other. This is probably related to the higher content of cells and vascularization in the peripheral zone, whereas the middle and inner zones of the meniscal body appear to be more similar to hyaline cartilage, with high levels of extracellular matrix proteins such as aggrecan and collagen type II.
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Affiliation(s)
- Elin Folkesson
- Faculty of Medicine, Department of Clinical Sciences Lund, Orthopaedics, Clinical Epidemiology UnitLund UniversityLund Sweden
- Faculty of Medicine, Department of Clinical Sciences Lund, Rheumatology and Molecular Skeletal BiologyLund UniversityLund Sweden
| | - Aleksandra Turkiewicz
- Faculty of Medicine, Department of Clinical Sciences Lund, Orthopaedics, Clinical Epidemiology UnitLund UniversityLund Sweden
| | - Martin Rydén
- Faculty of Medicine, Department of Clinical Sciences Lund, Orthopaedics, Clinical Epidemiology UnitLund UniversityLund Sweden
- Faculty of Medicine, Department of Clinical Sciences Lund, Rheumatology and Molecular Skeletal BiologyLund UniversityLund Sweden
| | - Harini Velocity Hughes
- Faculty of Medicine, Department of Clinical Sciences Lund, Orthopaedics, Clinical Epidemiology UnitLund UniversityLund Sweden
| | - Neserin Ali
- Faculty of Medicine, Department of Clinical Sciences Lund, Orthopaedics, Clinical Epidemiology UnitLund UniversityLund Sweden
| | - Jon Tjörnstrand
- Faculty of Medicine, Department of Clinical Sciences Lund, Orthopaedics, Clinical Epidemiology UnitLund UniversityLund Sweden
- Department of OrthopaedicsSkåne University HospitalLund Sweden
| | - Patrik Önnerfjord
- Faculty of Medicine, Department of Clinical Sciences Lund, Rheumatology and Molecular Skeletal BiologyLund UniversityLund Sweden
| | - Martin Englund
- Faculty of Medicine, Department of Clinical Sciences Lund, Orthopaedics, Clinical Epidemiology UnitLund UniversityLund Sweden
- Clinical Epidemiology Research and Training UnitBoston University School of MedicineBoston Massachusetts
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75
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Seabra G, de Almeida V, Reis-de-Oliveira G, Crunfli F, Antunes ASLM, Martins-de-Souza D. Ubiquitin-proteasome system, lipid metabolism and DNA damage repair are triggered by antipsychotic medication in human oligodendrocytes: implications in schizophrenia. Sci Rep 2020; 10:12655. [PMID: 32724114 PMCID: PMC7387551 DOI: 10.1038/s41598-020-69543-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/14/2020] [Indexed: 12/14/2022] Open
Abstract
Schizophrenia is a chronic, severe and disabling psychiatric disorder, whose treatment is based on psychosocial interventions and the use of antipsychotic drugs. While the effects of these drugs are well elucidated in neuronal cells, they are still not so clear in oligodendrocytes, which play a vital role in schizophrenia. Thus, we aimed to characterize biochemical profiles by proteomic analyses of human oligodendrocytes (MO3.13) which were matured using a protocol we developed and treated with either haloperidol (a typical antipsychotic), clozapine (an atypical antipsychotic) or a clozapine + D-serine co-treatment, which has emerged lately as an alternative type of treatment. This was accomplished by employing shotgun proteomics, using nanoESI-LC-MS/MS label-free quantitation. Proteomic analysis revealed biochemical pathways commonly affected by all tested antipsychotics were mainly associated to ubiquitination, proteasome degradation, lipid metabolism and DNA damage repair. Clozapine and haloperidol treatments also affected proteins involved with the actin cytoskeleton and with EIF2 signaling. In turn, metabolic processes, especially the metabolism of nitrogenous compounds, were a predominant target of modulation of clozapine + D-serine treatment. In this context, we seek to contribute to the understanding of the biochemical and molecular mechanisms involved in the action of antipsychotics on oligodendrocytes, along with their possible implications in schizophrenia.
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Affiliation(s)
- Gabriela Seabra
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Campinas, SP, 13083-862, Brazil
| | - Valéria de Almeida
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Campinas, SP, 13083-862, Brazil
| | - Guilherme Reis-de-Oliveira
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Campinas, SP, 13083-862, Brazil
| | - Fernanda Crunfli
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Campinas, SP, 13083-862, Brazil
| | - André Saraiva Leão Marcelo Antunes
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Campinas, SP, 13083-862, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Campinas, SP, 13083-862, Brazil.
- Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, SP, Brazil.
- D'Or Institute for Research and Education (IDOR), São Paulo, Brazil.
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76
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A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of this Field. Proteomes 2020; 8:proteomes8030014. [PMID: 32640657 PMCID: PMC7564415 DOI: 10.3390/proteomes8030014] [Citation(s) in RCA: 185] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/25/2020] [Accepted: 07/01/2020] [Indexed: 02/07/2023] Open
Abstract
Proteomics is the field of study that includes the analysis of proteins, from either a basic science prospective or a clinical one. Proteins can be investigated for their abundance, variety of proteoforms due to post-translational modifications (PTMs), and their stable or transient protein–protein interactions. This can be especially beneficial in the clinical setting when studying proteins involved in different diseases and conditions. Here, we aim to describe a bottom-up proteomics workflow from sample preparation to data analysis, including all of its benefits and pitfalls. We also describe potential improvements in this type of proteomics workflow for the future.
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77
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Wang D, Yang J, Fan J, Chen W, Nikolic‐Paterson DJ, Li J. Omics technologies for kidney disease research. Anat Rec (Hoboken) 2020; 303:2729-2742. [PMID: 32592293 DOI: 10.1002/ar.24413] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/31/2019] [Accepted: 02/17/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Dan Wang
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen University Guangzhou China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province Guangzhou China
| | - Jiayi Yang
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen University Guangzhou China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province Guangzhou China
| | - Jinjin Fan
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen University Guangzhou China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province Guangzhou China
| | - Wei Chen
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen University Guangzhou China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province Guangzhou China
| | | | - Jinhua Li
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen University Guangzhou China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province Guangzhou China
- Shunde Women and Children Hospital, Guangdong Medical University Shunde Guangdong China
- The Second Clinical College, Guangdong Medical University Dongguan Guangdong China
- Department of Anatomy and Developmental BiologyMonash Biomedicine Discovery Institute, Monash University Clayton Victoria Australia
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78
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Itze-Mayrhofer C, Brem G. Quantitative proteomic strategies to study reproduction in farm animals: Female reproductive fluids. J Proteomics 2020; 225:103884. [PMID: 32593762 DOI: 10.1016/j.jprot.2020.103884] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/10/2020] [Accepted: 06/21/2020] [Indexed: 02/06/2023]
Abstract
Reproductive fluids from the female reproductive tract are gaining attention for their potential to support and optimize reproductive processes, including gamete maturation and embryo culture in vitro. Quantitative proteomics is a powerful way to decipher the proteome of reproductive tract fluids and to identify biologically relevant proteins. The present review describes proteomic strategies for analysing female reproductive fluid proteins. In addition, it considers the strategies for the preparation of oviductal, uterine and follicular fluid samples. Finally, it highlights the main results of quantitative proteomic studies, providing insights into the biological processes related to reproductive biology in farm animals. SIGNIFICANCE: Assisted reproductive technologies (ARTs) have become vitally important for farm animal breeding and much effort is going into the optimization and refinement of the techniques. There are also attempts to imitate physiological conditions by adding reproductive fluids or individual fluid proteins to improve in vitro procedures. A detailed knowledge of the reproductive fluid proteomes is indispensable. The present review summarizes the most widely used quantitative proteomic approaches for the analysis of fluids from the female reproductive tract and highlights the potential of quantitative proteomics to delineate reproductive processes and identify candidate proteins for ARTs in farm animals.
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Affiliation(s)
- Corina Itze-Mayrhofer
- Institute of Animal Breeding and Genetics, Group Molecular Reproduction IFA-Tulln, University of Veterinary Medicine, Vienna, Austria.
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine, Vienna, Austria
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79
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Stultz LK, Hunsucker A, Middleton S, Grovenstein E, O'Leary J, Blatt E, Miller M, Mobley J, Hanson PK. Proteomic analysis of the S. cerevisiae response to the anticancer ruthenium complex KP1019. Metallomics 2020; 12:876-890. [PMID: 32329475 PMCID: PMC7362344 DOI: 10.1039/d0mt00008f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Like platinum-based chemotherapeutics, the anticancer ruthenium complex indazolium trans-[tetrachlorobis(1H-indazole)ruthenate(iii)], or KP1019, damages DNA, induces apoptosis, and causes tumor regression in animal models. Unlike platinum-based drugs, KP1019 showed no dose-limiting toxicity in a phase I clinical trial. Despite these advances, the mechanism(s) and target(s) of KP1019 remain unclear. For example, the drug may damage DNA directly or by causing oxidative stress. Likewise, KP1019 binds cytosolic proteins, suggesting DNA is not the sole target. Here we use the budding yeast Saccharomyces cerevisiae as a model in a proteomic study of the cellular response to KP1019. Mapping protein level changes onto metabolic pathways revealed patterns consistent with elevated synthesis and/or cycling of the antioxidant glutathione, suggesting KP1019 induces oxidative stress. This result was supported by increased fluorescence of the redox-sensitive dye DCFH-DA and increased KP1019 sensitivity of yeast lacking Yap1, a master regulator of the oxidative stress response. In addition to oxidative and DNA stress, bioinformatic analysis revealed drug-dependent increases in proteins involved ribosome biogenesis, translation, and protein (re)folding. Consistent with proteotoxic effects, KP1019 increased expression of a heat-shock element (HSE) lacZ reporter. KP1019 pre-treatment also sensitized yeast to oxaliplatin, paralleling prior research showing that cancer cell lines with elevated levels of translation machinery are hypersensitive to oxaliplatin. Combined, these data suggest that one of KP1019's many targets may be protein metabolism, which opens up intriguing possibilities for combination therapy.
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Affiliation(s)
- Laura K Stultz
- Department of Chemistry, Birmingham-Southern College, Birmingham, AL 35254, USA
| | - Alexandra Hunsucker
- Department of Biology, Birmingham-Southern College, Birmingham, AL 35254, USA
| | - Sydney Middleton
- Department of Chemistry, Birmingham-Southern College, Birmingham, AL 35254, USA
| | - Evan Grovenstein
- Department of Biology, Birmingham-Southern College, Birmingham, AL 35254, USA
| | - Jacob O'Leary
- Department of Chemistry, Birmingham-Southern College, Birmingham, AL 35254, USA
| | - Eliot Blatt
- Department of Biology, Rhodes College, Memphis, TN 38112, USA
| | - Mary Miller
- Department of Biology, Rhodes College, Memphis, TN 38112, USA
| | - James Mobley
- Department of Surgery, University of Alabama at Birmingham, School of Medicine, Birmingham, AL 35294, USA
| | - Pamela K Hanson
- Department of Biology, Furman University, Greenville, SC 29613, USA.
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Han Y, Tang C, Liao Q, Li Z, Deng L. Characterizing the Serum Proteome of Donkeys (Equus asinus). J Equine Vet Sci 2020; 92:103174. [PMID: 32797796 DOI: 10.1016/j.jevs.2020.103174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 11/18/2022]
Abstract
Serum and plasma are commonly used in clinical practice considering the widely accepted fact that the "normal" protein expression pattern of a healthy animal changes under disease conditions. We herein used a label-free mass spectrometry-based quantitative proteomics approach to characterize the serum proteome of donkeys. A total of 277 unique proteins were identified from 2,388 unique peptides. Gene ontology analyses showed that the most frequent processes were related to metabolic activities and biological regulation, response to stimulus, and immune system processes. The main annotated areas of origin were the extracellular region, extracellular region part, and organelle, and their molecular functions included binding, catalytic activity, and molecular function regulator. Analyses using the Clusters of Orthologous Groups for Eukaryotic Complete Genomes database indicated that the identified proteins could be categorized into three main groups: signal transduction mechanisms, amino acid transport and metabolism, and defense mechanisms. Most of the unique proteins were associated with the complement and coagulation cascades, and they participated in several disease-related metabolic pathways. Our results should be crucial for further analyses of changes in different physiological and pathophysiological conditions in donkeys.
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Affiliation(s)
- Yuwei Han
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, Liaoning Province, PR China
| | - Chi Tang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, Liaoning Province, PR China
| | - Qingchao Liao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, Liaoning Province, PR China
| | - Zheng Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, Liaoning Province, PR China
| | - Liang Deng
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, Liaoning Province, PR China.
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81
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Boukil A, Perreault V, Chamberland J, Mezdour S, Pouliot Y, Doyen A. High Hydrostatic Pressure-Assisted Enzymatic Hydrolysis Affect Mealworm Allergenic Proteins. Molecules 2020; 25:molecules25112685. [PMID: 32527059 PMCID: PMC7321092 DOI: 10.3390/molecules25112685] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/03/2020] [Accepted: 06/04/2020] [Indexed: 01/21/2023] Open
Abstract
Edible insects have garnered increased interest as alternative protein sources due to the world's growing population. However, the allergenicity of specific insect proteins is a major concern for both industry and consumers. This preliminary study investigated the capacity of high hydrostatic pressure (HHP) coupled to enzymatic hydrolysis by Alcalase® or pepsin in order to improve the in vitro digestion of mealworm proteins, specifically allergenic proteins. Pressurization was applied as pretreatment before in vitro digestion or, simultaneously, during hydrolysis. The degree of hydrolysis was compared between the different treatments and a mass spectrometry-based proteomic method was used to determine the efficiency of allergenic protein hydrolysis. Only the Alcalase® hydrolysis under pressure improved the degree of hydrolysis of mealworm proteins. Moreover, the in vitro digestion of the main allergenic proteins was increased by pressurization conditions that were specifically coupled to pepsin hydrolysis. Consequently, HHP-assisted enzymatic hydrolysis represents an alternative strategy to conventional hydrolysis for generating a large amount of peptide originating from allergenic mealworm proteins, and for lowering their immunoreactivity, for food, nutraceutical, and pharmaceutical applications.
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Affiliation(s)
- Abir Boukil
- Department of Food Sciences, Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC G1V 0A6, Canada; (A.B.); (V.P.); (J.C.); (Y.P.)
| | - Véronique Perreault
- Department of Food Sciences, Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC G1V 0A6, Canada; (A.B.); (V.P.); (J.C.); (Y.P.)
| | - Julien Chamberland
- Department of Food Sciences, Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC G1V 0A6, Canada; (A.B.); (V.P.); (J.C.); (Y.P.)
| | - Samir Mezdour
- AgroParisTech, UMR782 Paris-Saclay Food and Bioproduct Engineering (SayFood and Bioproduct Engineering), 1, rue des Olympiades, 91077 Massy, France;
| | - Yves Pouliot
- Department of Food Sciences, Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC G1V 0A6, Canada; (A.B.); (V.P.); (J.C.); (Y.P.)
| | - Alain Doyen
- Department of Food Sciences, Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC G1V 0A6, Canada; (A.B.); (V.P.); (J.C.); (Y.P.)
- Correspondence: ; Tel.: +1+418-656-2131 (ext. 4054540)
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82
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Pisanu S, Cacciotto C, Pagnozzi D, Uzzau S, Pollera C, Penati M, Bronzo V, Addis MF. Proteomic datasets of uninfected and Staphylococcus aureus-infected goat milk. Data Brief 2020; 30:105665. [PMID: 32426435 PMCID: PMC7225386 DOI: 10.1016/j.dib.2020.105665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 04/28/2020] [Indexed: 11/25/2022] Open
Abstract
We present a proteomic dataset generated from half-udder Alpine goat milk. The milk samples belonged to 3 groups: i) mid-lactation, low somatic cell count, uninfected milk (MLU, n=3); ii) late lactation, high somatic cell count, uninfected milk (LHU, n=3); and late lactation, high somatic cell count, Staphylococcus aureus subclinically infected milk (LHS, n=3). The detailed description of results is reported in the research article entitled “Impact of Staphylococcus aureus infection on the late lactation goat milk proteome: new perspectives for monitoring and understanding mastitis in dairy goats”. After milk defatting, high speed centrifugation and trypsin digestion of milk with the FASP protocol, peptide mixtures were analyzed by LC-MS/MS on a Q-Exactive. Peptide identification was carried out using Sequest-HT in Proteome Discoverer. Then, the Normalized Abundance Spectrum Factor (NSAF) value was calculated by label free quantitation using the spectral counting approach, and Gene Ontology (GO) annotation by Uniprot was carried out by reporting biological process, molecular function and cellular component. The MS data have been deposited to the ProteomeXchange via the PRIDE with the dataset identifier PXD017243.
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Affiliation(s)
| | | | | | - Sergio Uzzau
- Porto Conte Ricerche, Alghero, Italy
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
- Mediterranean Center for Disease Control, Sassari, Italy
| | - Claudia Pollera
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Martina Penati
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Valerio Bronzo
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Maria Filippa Addis
- Porto Conte Ricerche, Alghero, Italy
- Mediterranean Center for Disease Control, Sassari, Italy
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
- Corresponding author: Maria Filippa Addis, Department of Veterinary Medicine, University of Milan, Via dell'Università 6, 26900 Lodi (LO). Tel. ++39 02 503 34515
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83
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Pattipeiluhu R, Crielaard S, Klein-Schiphorst I, Florea BI, Kros A, Campbell F. Unbiased Identification of the Liposome Protein Corona using Photoaffinity-based Chemoproteomics. ACS CENTRAL SCIENCE 2020; 6:535-545. [PMID: 32342003 PMCID: PMC7181318 DOI: 10.1021/acscentsci.9b01222] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Indexed: 04/14/2023]
Abstract
Protein adsorption to the surface of a nanoparticle can fundamentally alter the character, behavior, and fate of a nanoparticle in vivo. Current methods to capture the protein corona rely on physical separation techniques and are unable to resolve key, individual protein-nanoparticle interactions. As a result, the precise link between the "synthetic" and the "biological" identity of a nanoparticle remains unclear. Herein, we report an unbiased photoaffinity-based approach to capture, characterize, and quantify the protein corona of liposomes in their native state. Compared to conventional methods, our photoaffinity approach reveals markedly different interacting proteins as well as reduced total protein binding to liposome surfaces. Identified proteins do not follow protein abundancy patterns of human serum, as has been generally reported, but are instead dominated by soluble apolipoproteins-endogenous serum proteins that have evolved to recognize the lipidic surface of circulating lipoproteins. We believe our findings are the most accurate characterization of a liposome's biological identity but, more fundamentally, reveal liposome-protein binding is, in many cases, significantly less complex than previously thought.
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Affiliation(s)
- Roy Pattipeiluhu
- Supramolecular
and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Stefan Crielaard
- Supramolecular
and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Iris Klein-Schiphorst
- Supramolecular
and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Bogdan I. Florea
- Bio-organic
Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Alexander Kros
- Supramolecular
and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333
CC Leiden, The Netherlands
- (A.K.)
| | - Frederick Campbell
- Supramolecular
and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333
CC Leiden, The Netherlands
- (F.C.)
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84
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Xu R, Greening DW, Chen M, Rai A, Ji H, Takahashi N, Simpson RJ. Surfaceome of Exosomes Secreted from the Colorectal Cancer Cell Line SW480: Peripheral and Integral Membrane Proteins Analyzed by Proteolysis and TX114. Proteomics 2020; 19:e1700453. [PMID: 30865381 DOI: 10.1002/pmic.201700453] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 02/18/2019] [Indexed: 12/11/2022]
Abstract
Exosomes are important bidirectional cell-cell communicators in normal and pathological physiology. Although exosomal surface membrane proteins (surfaceome) enable target cell recognition and are an attractive source of disease marker, they are poorly understood. Here, a comprehensive surfaceome analysis of exosomes secreted by the colorectal cancer cell line SW480 is described. Sodium carbonate extraction/Triton X-114 phase separation and mild proteolysis (proteinase K, PK) of intact exosomes is used in combination with label-free quantitative mass spectrometry to identify 1025 exosomal proteins of which 208 are predicted to be integral membrane proteins (IMPs) according to TOPCONS and GRAVY scores. Interrogation of UniProt database-annotated proteins reveals 124 predicted peripherally-associated membrane proteins (PMPs). Surprisingly, 108 RNA-binding proteins (RBPs)/RNA nucleoproteins (RNPs) are found in the carbonate/Triton X-114 insoluble fraction. Mild PK treatment of SW480-GFP labeled exosomes reveal 58 proteolytically cleaved IMPs and 14 exoplasmic PMPs (e.g., CLU/GANAB/LGALS3BP). Interestingly, 18 RBPs/RNPs (e.g., EIF3L/RPL6) appear bound to the outer exosome surface since they are sensitive to PK proteolysis. The finding that outer surface-localized miRNA Let-7a-5p is RNase A-resistant, but degraded by a combination of RNase A/PK treatment suggests exosomal miRNA species also reside on the outer surface of exosomes bound to RBPs/RNPs.
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Affiliation(s)
- Rong Xu
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, 3086, Australia
| | - David W Greening
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Maoshan Chen
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Alin Rai
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Hong Ji
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Nobuhiro Takahashi
- Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu City, Tokyo, 183-8509, Japan.,Global Innovation Research Organization, Tokyo University of Agriculture and Technology, Fuchu City, Tokyo, 183-8538, Japan
| | - Richard J Simpson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, 3086, Australia.,Global Innovation Research Organization, Tokyo University of Agriculture and Technology, Fuchu City, Tokyo, 183-8538, Japan
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85
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Wu J, Zhang J, Wei J, Zhao Y, Gao Y. Urinary biomarker discovery in gliomas using mass spectrometry-based clinical proteomics. Chin Neurosurg J 2020; 6:11. [PMID: 32922940 PMCID: PMC7398313 DOI: 10.1186/s41016-020-00190-5] [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: 11/13/2019] [Accepted: 03/18/2020] [Indexed: 02/07/2023] Open
Abstract
Background Gliomas are the most common primary malignant brain tumors and have a poor prognosis. Early detection of gliomas is crucial to improve patient outcomes. Urine accumulates systematic body changes and thus serves as an excellent early biomarker source. Methods At the biomarker discovery phase, we performed a self-controlled proteomics analysis by comparing urine samples collected from five glioma patients at the time of tumor diagnosis and after surgical removal of the tumor. At the biomarker validation phase, we further validated some promising proteins using parallel reaction monitoring (PRM)-based targeted proteomics in another cohort, including glioma, meningioma, and moyamoya disease patients as well as healthy controls. Results Using label-free proteome quantitation (LFQ), we identified twenty-seven urinary proteins that were significantly changed after tumor resection, many of which have been previously associated with gliomas. The functions of these proteins were significantly enriched in the autophagy and angiogenesis, which are associated with glioma development. After targeted proteomics validation, we identified a biomarker panel (AACT, TSP4, MDHM, CALR, LEG1, and AHSG) with an area under the curve (AUC) value of 0.958 for the detection of gliomas. Interestingly, AACT, LEG1, and AHSG are also potential cerebrospinal fluid or blood biomarkers of gliomas. Conclusions Using LFQ and PRM proteome quantification, we identified candidate urinary protein biomarkers with the potential to detect gliomas. This study will also provide clues for future biomarker studies involving brain diseases.
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Affiliation(s)
- Jianqiang Wu
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730 China
| | - Jun Zhang
- Department of Neurosurgery, Peking University International Hospital, Peking University, Beijing, 102206 China
| | - Jing Wei
- Department of Biochemistry, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, School of Life Sciences, Beijing Normal University, No.19 Xinjiekouwai Street, Beijing, 100875 China
| | - Yuanli Zhao
- Department of Neurosurgery, Peking University International Hospital, Peking University, Beijing, 102206 China.,Department of Neurosurgery, Beijing Tian Tan Hospital, Capital Medical University; China National Clinical Research Center for Neurological Diseases, Beijing, 100050 China
| | - Youhe Gao
- Department of Biochemistry, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, School of Life Sciences, Beijing Normal University, No.19 Xinjiekouwai Street, Beijing, 100875 China
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86
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Impact of Staphylococcus aureus infection on the late lactation goat milk proteome: New perspectives for monitoring and understanding mastitis in dairy goats. J Proteomics 2020; 221:103763. [PMID: 32275959 DOI: 10.1016/j.jprot.2020.103763] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/03/2020] [Accepted: 03/28/2020] [Indexed: 12/30/2022]
Abstract
The milk somatic cell count (SCC) is a standard parameter for monitoring intramammary infections (IMI) in dairy ruminants. In goats, however, the physiological increase in SCC occurring in late lactation heavily compromises its reliability. To identify and understand milk protein changes specifically related to IMI, we carried out a shotgun proteomics study comparing high SCC late lactation milk from goats with subclinical Staphylococcus aureus IMI and from healthy goats to low SCC mid-lactation milk from healthy goats. As a result, we detected 52 and 19 differential proteins (DPs) in S. aureus-infected and uninfected late lactation milk, respectively. Unexpectedly, one of the proteins higher in uninfected milk was serum amyloid A. On the other hand, 38 DPs were increased only in S. aureus-infected milk and included haptoglobin and numerous cytoskeletal proteins. Based on STRING analysis, the DPs unique to S. aureus infected milk were mainly involved in defense response, cytoskeleton organization, cell-to-cell, and cell-to-matrix interactions. Being tightly and specifically related to infectious/inflammatory processes, these proteins may hold promise as more reliable markers of IMI than SCC in late lactation goats. SIGNIFICANCE: The biological relevance of our results lies in the increased understanding of the changes specifically related to bacterial infection of the goat udder in late lactation. The DPs present only in S. aureus infected milk may find application as markers for improving the specificity of subclinical mastitis monitoring and detection in dairy goats in late lactation, when other widespread tools such as the SCC lose diagnostic value.
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87
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Xu G, Fromholt SE, Chakrabarty P, Zhu F, Liu X, Pace MC, Koh J, Golde TE, Levites Y, Lewis J, Borchelt DR. Diversity in Aβ deposit morphology and secondary proteome insolubility across models of Alzheimer-type amyloidosis. Acta Neuropathol Commun 2020; 8:43. [PMID: 32252825 PMCID: PMC7137436 DOI: 10.1186/s40478-020-00911-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/02/2020] [Indexed: 12/30/2022] Open
Abstract
A hallmark pathology of Alzheimer's disease (AD) is the formation of amyloid β (Aβ) deposits that exhibit diverse localization and morphologies, ranging from diffuse to cored-neuritic deposits in brain parenchyma, with cerebral vascular deposition in leptomeningeal and parenchymal compartments. Most AD brains exhibit the full spectrum of pathologic Aβ morphologies. In the course of studies to model AD amyloidosis, we have generated multiple transgenic mouse models that vary in the nature of the transgene constructs that are expressed; including the species origin of Aβ peptides, the levels and length of Aβ that is deposited, and whether mutant presenilin 1 (PS1) is co-expressed. These models recapitulate features of human AD amyloidosis, but interestingly some models can produce pathology in which one type of Aβ morphology dominates. In prior studies of mice that primarily develop cored-neuritic deposits, we determined that Aβ deposition is associated with changes in cytosolic protein solubility in which a subset of proteins become detergent-insoluble, indicative of secondary proteome instability. Here, we survey changes in cytosolic protein solubility across seven different transgenic mouse models that exhibit a range of Aβ deposit morphologies. We find a surprisingly diverse range of changes in proteome solubility across these models. Mice that deposit human Aβ40 and Aβ42 in cored-neuritic plaques had the most robust changes in proteome solubility. Insoluble cytosolic proteins were also detected in the brains of mice that develop diffuse Aβ42 deposits but to a lesser extent. Notably, mice with cored deposits containing only Aβ42 had relatively few proteins that became detergent-insoluble. Our data provide new insight into the diversity of biological effects that can be attributed to different types of Aβ pathology and support the view that fibrillar cored-neuritic plaque pathology is the more disruptive Aβ pathology in the Alzheimer's cascade.
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Affiliation(s)
- Guilian Xu
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Susan E Fromholt
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Paramita Chakrabarty
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Fanchao Zhu
- The Interdisciplinary Center for Biotechnology Research (ICBR), University of Florida, Gainesville, FL, 32610, USA
| | - Xuefei Liu
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Michael C Pace
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Jin Koh
- The Interdisciplinary Center for Biotechnology Research (ICBR), University of Florida, Gainesville, FL, 32610, USA
| | - Todd E Golde
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Yona Levites
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Jada Lewis
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - David R Borchelt
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA.
- SantaFe Healthcare Alzheimer's Disease Research Center, Gainesville, FL, USA.
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88
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Zhao S, An B, Guo Y, Hou X, Luo H, He C, Wang Q. Label free proteomics and systematic analysis of secretome reveals effector candidates regulated by SGE1 and FTF1 in the plant pathogen Fusarium oxysporum f. sp. cubense tropical race 4. BMC Genomics 2020; 21:275. [PMID: 32245409 PMCID: PMC7119298 DOI: 10.1186/s12864-020-6695-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/24/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Phytopathogens secreted effectors during host colonization to suppress or trigger plant immunity. Identification of new effectors is one of the research focuses in recent years. There is only a limited knowledge about effectors of Fusarium oxysporum f. sp. Cubense tropical race 4 (Foc TR4), the causal agent of wilt disease in Cavendish banana. RESULTS Two transcription factors, SGE1 and FTF1, were constitutively over-expressed in Foc TR4 to partially mimic the in-planta state. Secreted proteins with high purity were prepared through a two-round extraction method. Then the secretome were analyzed via label free proteomics method. A total of 919 non-redundant proteins were detected, of which 74 proteins were predicted to be effector candidates. Among these candidates, 29 were up-regulated and 13 down-regulated in the strain over-expressing SGE1 and FTF1, 8 were up-regulated and 4 down-regulated in either SGE1 or FTF1 over expression strain. CONCLUSIONS Through label free proteomics analysis, a series of effector candidates were identified in secretome of Foc TR4. Our work put a foundation for functional research of these effectors.
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Affiliation(s)
- Shixue Zhao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, Hainan, 570228, People's Republic of China
| | - Bang An
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, Hainan, 570228, People's Republic of China
| | - Yanhua Guo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, Hainan, 570228, People's Republic of China
| | - Xingrong Hou
- College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, Hainan, 572022, People's Republic of China
| | - Hongli Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, Hainan, 570228, People's Republic of China
| | - Chaozu He
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, Hainan, 570228, People's Republic of China
| | - Qiannan Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, Hainan, 570228, People's Republic of China.
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Proteomic Profiles and Biological Processes of Relapsed vs. Non-Relapsed Pediatric Hodgkin Lymphoma. Int J Mol Sci 2020; 21:ijms21062185. [PMID: 32235718 PMCID: PMC7139997 DOI: 10.3390/ijms21062185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 03/19/2020] [Indexed: 12/12/2022] Open
Abstract
The identification of circulating proteins associated with relapse in pediatric Hodgkin lymphoma (HL) may help develop predictive biomarkers. We previously identified a set of predictive biomarkers by difference gel electrophoresis. Here we used label-free quantitative liquid chromatography-mass spectrometry (LC-MS/MS) on plasma collected at diagnosis from 12 children (age 12–16 years) with nodular sclerosis HL, including six in whom the disease relapsed within 5 years of treatment in the LH2004 trial. Plasma proteins were pooled in groups of three, separately for non-relapsing and relapsing HL, and differentially abundant proteins between the two disease states were identified by LC-MS/MS in an explorative and validation design. Proteins with a fold change in abundance >1.2 or ≤0.8 were considered “differentially abundant”. LC-MS/MS identified 60 and 32 proteins that were more abundant in non-relapsing and relapsing HL plasma, respectively, in the explorative phase; these numbers were 39 and 34 in the validation phase. In both analyses, 11 proteins were more abundant in non-relapsing HL (e.g., angiotensinogen, serum paraoxonase/arylesterase 1, transthyretin), including two previously identified by difference gel electrophoresis (antithrombin III and α-1-antitrypsin); seven proteins were more abundant in relapsing HL (e.g., fibronectin and thrombospondin-1), including two previously identified proteins (fibrinogen β and γ chains). The differentially abundant proteins participated in numerous biological processes, which were manually grouped into 10 biological classes and 11 biological regulatory subclasses. The biological class Lipid metabolism, and its regulatory subclass, included angiotensinogen and serum paraoxonase/arylesterase 1 (more abundant in non-relapsing HL). The biological classes Immune system and Cell and extracellular matrix architecture included fibronectin and thrombospondin-1 (more abundant in relapsing HL). These findings deepen our understanding of the molecular scenario underlying responses to therapy and provide new evidence about these proteins as possible biomarkers of relapse in pediatric HL.
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90
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Larsen MH, Lacourciere K, Parker TM, Kraigsley A, Achkar JM, Adams LB, Dupnik KM, Hall-Stoodley L, Hartman T, Kanipe C, Kurtz SL, Miller MA, Salvador LCM, Spencer JS, Robinson RT. The Many Hosts of Mycobacteria 8 (MHM8): A conference report. Tuberculosis (Edinb) 2020; 121:101914. [PMID: 32279870 PMCID: PMC7428850 DOI: 10.1016/j.tube.2020.101914] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/07/2020] [Accepted: 02/09/2020] [Indexed: 12/18/2022]
Abstract
Mycobacteria are important causes of disease in human and animal hosts. Diseases caused by mycobacteria include leprosy, tuberculosis (TB), nontuberculous mycobacteria (NTM) infections and Buruli Ulcer. To better understand and treat mycobacterial disease, clinicians, veterinarians and scientists use a range of discipline-specific approaches to conduct basic and applied research, including conducting epidemiological surveys, patient studies, wildlife sampling, animal models, genetic studies and computational simulations. To foster the exchange of knowledge and collaboration across disciplines, the Many Hosts of Mycobacteria (MHM) conference series brings together clinical, veterinary and basic scientists who are dedicated to advancing mycobacterial disease research. Started in 2007, the MHM series recently held its 8th conference at the Albert Einstein College of Medicine (Bronx, NY). Here, we review the diseases discussed at MHM8 and summarize the presentations on research advances in leprosy, NTM and Buruli Ulcer, human and animal TB, mycobacterial disease comorbidities, mycobacterial genetics and 'omics, and animal models. A mouse models workshop, which was held immediately after MHM8, is also summarized. In addition to being a resource for those who were unable to attend MHM8, we anticipate this review will provide a benchmark to gauge the progress of future research concerning mycobacteria and their many hosts.
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Affiliation(s)
- Michelle H Larsen
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Karen Lacourciere
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20892, USA
| | - Tina M Parker
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20892, USA
| | - Alison Kraigsley
- Center for Infectious Disease Research and Policy, University of Minnesota, Minneapolis, MN, USA
| | - Jacqueline M Achkar
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Linda B Adams
- Department of Health and Human Services, Health Resources and Services Administration, Healthcare Systems Bureau, National Hansen's Disease Programs, Baton Rouge, LA, USA
| | - Kathryn M Dupnik
- Center for Global Health, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Luanne Hall-Stoodley
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Travis Hartman
- Center for Global Health, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Carly Kanipe
- Department of Immunobiology, Iowa State University, Ames, IA, USA; Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA; Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA
| | - Sherry L Kurtz
- Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Washington, DC, USA
| | - Michele A Miller
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Liliana C M Salvador
- Department of Infectious Diseases, University of Georgia, Athens, GA, USA; Institute of Bioinformatics, University of Georgia, Athens, GA, USA; Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - John S Spencer
- Department of Microbiology, Immunology, and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO, USA
| | - Richard T Robinson
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA.
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91
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Mullins Y, Keogh K, Kenny DA, Kelly A, O' Boyle P, Waters SM. Label-free quantitative proteomic analysis of M. longissimus dorsi from cattle during dietary restriction and subsequent compensatory growth. Sci Rep 2020; 10:2613. [PMID: 32054912 PMCID: PMC7018817 DOI: 10.1038/s41598-020-59412-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 01/18/2020] [Indexed: 12/12/2022] Open
Abstract
Compensatory growth (CG) is a naturally occurring physiological process whereby an animal has the ability to undergo enhanced growth following a period of restricted feeding. This studies objective was to identify key proteins involved in the expression of CG. Forty Holstein Friesian bulls were equally assigned to one of four groups. R1 and R2 groups were subjected to restricted feed allowance for 125 days (Period 1). A1 and A2 animals had ad libitum access to feed in Period 1. Following Period 1, all animals from R1 and A1 were slaughtered. Remaining animals (R2 and A2) were slaughtered following ad libitum access to feed for successive 55 days (Period 2). M. longissimus dorsi samples were collected at slaughter from all animals. Proteins were isolated from samples and subjected to label-free mass spectrometry proteomic quantification. Proteins which were differentially abundant during CG (n = 39) were involved in cellular binding processes, oxidative phosphorylation and mitochondrial function. There was also evidence for up regulation of three pathways involved in nucleotide biosynthesis. Genetic variants in or regulating genes pertaining to proteins identified in this study may hold potential for use as DNA based biomarkers for genomic selection of animals with a greater ability to undergo CG.
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Affiliation(s)
- Yvonne Mullins
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co., Meath, Ireland.,School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Kate Keogh
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co., Meath, Ireland
| | - David A Kenny
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co., Meath, Ireland
| | - Alan Kelly
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Padraig O' Boyle
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Athenry, Co., Galway, Ireland
| | - Sinéad M Waters
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co., Meath, Ireland.
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92
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Kögler M, Itkonen J, Viitala T, Casteleijn MG. Assessment of recombinant protein production in E. coli with Time-Gated Surface Enhanced Raman Spectroscopy (TG-SERS). Sci Rep 2020; 10:2472. [PMID: 32051493 PMCID: PMC7015922 DOI: 10.1038/s41598-020-59091-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/23/2020] [Indexed: 01/18/2023] Open
Abstract
Time-Gated Surface-Enhanced Raman spectroscopy (TG-SERS) was utilized to assess recombinant protein production in Escherichia coli. TG-SERS suppressed the fluorescence signal from the biomolecules in the bacteria and the culture media. Characteristic protein signatures at different time points of the cell cultivation were observed and compared to conventional continuous wave (CW)-Raman with SERS. TG-SERS can distinguish discrete features of proteins such as the secondary structures and is therefore indicative of folding or unfolding of the protein. A novel method utilizing nanofibrillar cellulose as a stabilizing agent for nanoparticles and bacterial cells was used for the first time in order to boost the Raman signal, while simultaneously suppressing background signals. We evaluated the expression of hCNTF, hHspA1, and hHsp27 in complex media using the batch fermentation mode. HCNTF was also cultivated using EnBase in a fed-batch like mode. HspA1 expressed poorly due to aggregation problems within the cell, while hCNTF expressed in batch mode was correctly folded and protein instabilities were identified in the EnBase cultivation. Time-gated Raman spectroscopy showed to be a powerful tool to evaluate protein production and correct folding within living E. coli cells during the cultivation.
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Affiliation(s)
- Martin Kögler
- VTT Technical Research Centre of Finland, Oulu, Finland
| | - Jaakko Itkonen
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Tapani Viitala
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Marco G Casteleijn
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland. .,VTT Technical Research Centre of Finland, Espoo, Finland.
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93
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Ertekin O, Kutnu M, Taşkin AA, Demir M, Karataş AY, Özcengiz G. Analysis of a bac operon-silenced strain suggests pleiotropic effects of bacilysin in Bacillus subtilis. J Microbiol 2020; 58:297-313. [DOI: 10.1007/s12275-020-9064-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 12/11/2019] [Accepted: 12/24/2019] [Indexed: 11/24/2022]
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94
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Biberoglu K, Tacal O, Schopfer LM, Lockridge O. Chlorpyrifos Oxon-Induced Isopeptide Bond Formation in Human Butyrylcholinesterase. Molecules 2020; 25:molecules25030533. [PMID: 31991818 PMCID: PMC7037448 DOI: 10.3390/molecules25030533] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 11/16/2022] Open
Abstract
A newly recognized action of organophosphates (OP) is the ability to crosslink proteins through an isopeptide bond. The first step in the mechanism is covalent addition of the OP to the side chain of lysine. This activates OP-lysine for reaction with a nearby glutamic or aspartic acid to make a gamma glutamyl epsilon lysine bond. Crosslinked proteins are high molecular weight aggregates. Our goal was to identify the residues in the human butyrylcholinesterase (HuBChE) tetramer that were crosslinked following treatment with 1.5 mM chlorpyrifos oxon. High molecular weight bands were visualized on an SDS gel. Proteins in the gel bands were digested with trypsin, separated by liquid chromatography and analyzed in an Orbitrap mass spectrometer. MSMS files were searched for crosslinked peptides using the Batch-Tag program in Protein Prospector. MSMS spectra were manually evaluated for the presence of ions that supported the crosslinks. The crosslink between Lys544 in VLEMTGNIDEAEWEWK544AGFHR and Glu542 in VLEMTGNIDEAEWE542WK satisfied our criteria including that of spatial proximity. Distances between Lys544 and Glu542 were 7.4 and 9.5 Å, calculated from the cryo-EM (electron microscopy) structure of the HuBChE tetramer. Paraoxon ethyl, diazoxon, and dichlorvos had less pronounced effects as visualized on SDS gels. Our proof-of-principle study provides evidence that OP have the ability to crosslink proteins. If OP-induced protein crosslinking occurs in the brain, OP exposure could be responsible for some cases of neurodegenerative disease.
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Affiliation(s)
- Kevser Biberoglu
- Department of Biochemistry, School of Pharmacy, Hacettepe University, Ankara 06230, Turkey; (K.B.); (O.T.)
| | - Ozden Tacal
- Department of Biochemistry, School of Pharmacy, Hacettepe University, Ankara 06230, Turkey; (K.B.); (O.T.)
| | - Lawrence M. Schopfer
- Eppley Institute, University of Nebraska Medical Center, Omaha, NE 68198-5900, USA;
- Correspondence: ; Tel.: 1-402-559-6305
| | - Oksana Lockridge
- Eppley Institute, University of Nebraska Medical Center, Omaha, NE 68198-5900, USA;
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95
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Kawaguchi T, Rollins MG, Moinpour M, Morera AA, Ebmeier CC, Old WM, Schwartz JC. Changes to the TDP-43 and FUS Interactomes Induced by DNA Damage. J Proteome Res 2020; 19:360-370. [PMID: 31693373 PMCID: PMC6947635 DOI: 10.1021/acs.jproteome.9b00575] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Indexed: 12/13/2022]
Abstract
The RNA-binding proteins TDP-43 and FUS are tied as the third leading known genetic cause for amyotrophic lateral sclerosis (ALS), and TDP-43 proteopathies are found in nearly all ALS patients. Both the natural function and contribution to pathology for TDP-43 remain unclear. The intersection of functions between TDP-43 and FUS can focus attention for those natural functions mostly likely to be relevant to disease. Here, we compare the role played by TDP-43 and FUS, maintaining chromatin stability for dividing HEK293T cells. We also determine and compare the interactomes of TDP-43 and FUS, quantitating changes in those before and after DNA damage. Finally, selected interactions with known importance to DNA damage repair were validated by co-immunoprecipitation assays. This study uncovered TDP-43 and FUS binding to several factors important to DNA repair mechanisms that can be replication-dependent, -independent, or both. These results provide further evidence that TDP-43 has an important role in DNA stability and provide new ways that TDP-43 can bind to the machinery that guards DNA integrity in cells.
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Affiliation(s)
- Tetsuya Kawaguchi
- Department
of Chemistry and Biochemistry and Department of Molecular and Cellular
Biology, University of Arizona, Tucson, Arizona 85721, United States
| | - Matthew G. Rollins
- Department
of Chemistry and Biochemistry and Department of Molecular and Cellular
Biology, University of Arizona, Tucson, Arizona 85721, United States
| | - Mahta Moinpour
- Department
of Chemistry and Biochemistry and Department of Molecular and Cellular
Biology, University of Arizona, Tucson, Arizona 85721, United States
| | - Andres A. Morera
- Department
of Chemistry and Biochemistry and Department of Molecular and Cellular
Biology, University of Arizona, Tucson, Arizona 85721, United States
| | - Christopher C. Ebmeier
- Department
of Molecular and Cellular Biology, University
of Colorado, Boulder, Colorado 80309, United States
| | - William M. Old
- Department
of Molecular and Cellular Biology, University
of Colorado, Boulder, Colorado 80309, United States
| | - Jacob C. Schwartz
- Department
of Chemistry and Biochemistry and Department of Molecular and Cellular
Biology, University of Arizona, Tucson, Arizona 85721, United States
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96
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Liu J, Hao C, Wu L, Madej D, Chan W, Lam H. Proteomic analysis of thioproline misincorporation in Escherichia coli. J Proteomics 2020; 210:103541. [DOI: 10.1016/j.jprot.2019.103541] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 09/27/2019] [Accepted: 10/07/2019] [Indexed: 01/01/2023]
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97
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Palrasu M, Knapinska AM, Diez J, Smith L, LaVoi T, Giulianotti M, Houghten RA, Fields GB, Minond D. A Novel Probe for Spliceosomal Proteins that Induces Autophagy and Death of Melanoma Cells Reveals New Targets for Melanoma Drug Discovery. Cell Physiol Biochem 2019; 53:656-686. [PMID: 31573152 PMCID: PMC6990463 DOI: 10.33594/000000164] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 09/25/2019] [Indexed: 12/24/2022] Open
Abstract
Background/Aims: Despite recent advances in melanoma drug discovery, the average overall survival of patients with late stage metastatic melanoma is approximately 3 years, suggesting a need for approaches that identify new melanoma targets. We have previously reported a discovery of novel anti-melanoma compound 2155–14 (Onwuha-Ekpete et al., J Med Chem. 2014 Feb 27; 57(4):1599–608). In the report presented herein we aim to identify its target(s) and mechanism of action. Methods: We utilized biotinylated analog of 2155–14 to pull down its targets from melanoma cells. Proteomics in combination with western blot were used to identify the targets. Mechanism of action of 2155–14 was determined using flow cytometry, RT-PCR, microscopy, western blot, and enzymatic activity assays. Where applicable, one-way analysis of variance (ANOVA) was used followed by Dunnett post hoc test. Results: In the present study, we identified ATP-dependent RNA helicase DDX1 and heterogeneous nuclear ribonucleoproteins (hnRNPs) H1, H2 and A2/B1 as targets of anti-melanoma compound 2155–14. To the best of our knowledge, this is a first report suggesting that these proteins could be targeted for melanoma therapy. Mechanistic investigations showed that 2155–14 induces ER stress leading to potentiation of basal autophagy resulting in melanoma cell death in BRAF and NRAS mutated melanoma cells. Conclusion: Identification of mode of action of 2155–14 may provide insight into novel therapies against a broad range of melanoma subtypes. These studies were enabled by the novel probe derived from a mixture-based library, an important class of chemical biology tools for discovering novel targets.
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Affiliation(s)
- Manikandan Palrasu
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
| | - Anna M Knapinska
- Department of Chemistry & Biochemistry, Center for Molecular Biology & Biotechnology, Florida Atlantic University, Jupiter, FL, USA
| | - Juan Diez
- Rumbaugh-Goodwin Institute for Cancer Research, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Lyndsay Smith
- Department of Chemistry & Biochemistry, Center for Molecular Biology & Biotechnology, Florida Atlantic University, Jupiter, FL, USA
| | - Travis LaVoi
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, FL, USA
| | - Marc Giulianotti
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, FL, USA
| | | | - Gregg B Fields
- Department of Chemistry & Biochemistry, Center for Molecular Biology & Biotechnology, Florida Atlantic University, Jupiter, FL, USA
| | - Dmitriy Minond
- Rumbaugh-Goodwin Institute for Cancer Research, Nova Southeastern University, Fort Lauderdale, FL, USA.,Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, USA,
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98
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Otake H, Yamamoto T, Deguchi S, Taga A, Nagai N. Retinal proteomic evaluation of rats following streptozotocin‑injection using shotgun proteomics. Mol Med Rep 2019; 21:379-386. [PMID: 31746385 DOI: 10.3892/mmr.2019.10801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/24/2019] [Indexed: 11/05/2022] Open
Abstract
It is important to elucidate how retinal stimulation leads to retinal protection and dysfunction. The current study aimed to identify factors that are up‑ and downregulated in the retinas of streptozotocin (STZ)‑induced diabetic rats with acute retinal dysfunction. Retinal function was measured and changes in protein expressions were determined using electroretinograms (ERGs) and liquid chromatography/mass spectroscopy‑based shotgun proteomics, respectively. The results revealed that the plasma glucose levels of STZ rats were markedly higher when compared with normal rats. Furthermore, levels of a‑waves, b‑waves and oscillatory potential amplitudes on ERGs in STZ rats were decreased compared with healthy animals. With use of shotgun proteomics, 391 proteins were identified in the retinas of normal rats and 541 proteins were found in the retinas of STZ rats. Of the 560 proteins identified in rat retinas, 372 (66.4%) were present in both normal and STZ rats. Of these, 19 (3.39%) were unique to normal rats and 169 (30.1%) were unique to STZ rats. Gene Ontology analysis was performed on the candidate proteins that were differentially regulated in the retinas of STZ rats and focused on those classified as 'protein binding', which serve important roles in retinal neurodegeneration. The results revealed an excessive expression of retinol‑binding protein 1 (RBP1) and a negative expression of rod outer segment membrane protein 1 (Rom-1) in the retinas of STZ rats. Therefore, retinal function may be decreased with STZ‑induced injury, and expressions of Rom‑1 and RBP1 may be altered in the retinas of STZ rats.
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Affiliation(s)
- Hiroko Otake
- Faculty of Pharmacy, Kindai University, Higashi-Osaka, Osaka 577‑8502, Japan
| | - Tetushi Yamamoto
- Faculty of Pharmacy, Kindai University, Higashi-Osaka, Osaka 577‑8502, Japan
| | - Saori Deguchi
- Faculty of Pharmacy, Kindai University, Higashi-Osaka, Osaka 577‑8502, Japan
| | - Atushi Taga
- Faculty of Pharmacy, Kindai University, Higashi-Osaka, Osaka 577‑8502, Japan
| | - Noriaki Nagai
- Faculty of Pharmacy, Kindai University, Higashi-Osaka, Osaka 577‑8502, Japan
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99
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Pisanu S, Cacciotto C, Pagnozzi D, Puggioni GMG, Uzzau S, Ciaramella P, Guccione J, Penati M, Pollera C, Moroni P, Bronzo V, Addis MF. Proteomic changes in the milk of water buffaloes (Bubalus bubalis) with subclinical mastitis due to intramammary infection by Staphylococcus aureus and by non-aureus staphylococci. Sci Rep 2019; 9:15850. [PMID: 31676851 PMCID: PMC6825138 DOI: 10.1038/s41598-019-52063-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 10/08/2019] [Indexed: 02/07/2023] Open
Abstract
Subclinical mastitis by Staphylococcus aureus (SAU) and by non-aureus staphylococci (NAS) is a major issue in the water buffalo. To understand its impact on milk, 6 quarter samples with >3,000,000 cells/mL (3 SAU-positive and 3 NAS-positive) and 6 culture-negative quarter samples with <50,000 cells/mL were investigated by shotgun proteomics and label-free quantitation. A total of 1530 proteins were identified, of which 152 were significantly changed. SAU was more impacting, with 162 vs 127 differential proteins and higher abundance changes (P < 0.0005). The 119 increased proteins had mostly structural (n = 43, 28.29%) or innate immune defence functions (n = 39, 25.66%) and included vimentin, cathelicidins, histones, S100 and neutrophil granule proteins, haptoglobin, and lysozyme. The 33 decreased proteins were mainly involved in lipid metabolism (n = 13, 59.10%) and included butyrophilin, xanthine dehydrogenase/oxidase, and lipid biosynthetic enzymes. The same biological processes were significantly affected also upon STRING analysis. Cathelicidins were the most increased family, as confirmed by western immunoblotting, with a stronger reactivity in SAU mastitis. S100A8 and haptoglobin were also validated by western immunoblotting. In conclusion, we generated a detailed buffalo milk protein dataset and defined the changes occurring in SAU and NAS mastitis, with potential for improving detection (ProteomeXchange identifier PXD012355).
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Affiliation(s)
| | - Carla Cacciotto
- Porto Conte Ricerche, Alghero, Italy.,Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Sassari, Italy
| | | | | | - Sergio Uzzau
- Porto Conte Ricerche, Alghero, Italy.,Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
| | - Paolo Ciaramella
- Dipartimento di Medicina Veterinaria e Produzioni Animali, Università di Napoli Federico II, Naples, Italy
| | - Jacopo Guccione
- Dipartimento di Medicina Veterinaria e Produzioni Animali, Università di Napoli Federico II, Naples, Italy
| | - Martina Penati
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Claudia Pollera
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Paolo Moroni
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy.,Animal Health Diagnostic Center, Cornell University, Ithaca, NY, USA
| | - Valerio Bronzo
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Maria Filippa Addis
- Porto Conte Ricerche, Alghero, Italy. .,Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy.
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100
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Wang X, Shen S, Rasam SS, Qu J. MS1 ion current-based quantitative proteomics: A promising solution for reliable analysis of large biological cohorts. MASS SPECTROMETRY REVIEWS 2019; 38:461-482. [PMID: 30920002 PMCID: PMC6849792 DOI: 10.1002/mas.21595] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/28/2019] [Indexed: 05/04/2023]
Abstract
The rapidly-advancing field of pharmaceutical and clinical research calls for systematic, molecular-level characterization of complex biological systems. To this end, quantitative proteomics represents a powerful tool but an optimal solution for reliable large-cohort proteomics analysis, as frequently involved in pharmaceutical/clinical investigations, is urgently needed. Large-cohort analysis remains challenging owing to the deteriorating quantitative quality and snowballing missing data and false-positive discovery of altered proteins when sample size increases. MS1 ion current-based methods, which have become an important class of label-free quantification techniques during the past decade, show considerable potential to achieve reproducible protein measurements in large cohorts with high quantitative accuracy/precision. Nonetheless, in order to fully unleash this potential, several critical prerequisites should be met. Here we provide an overview of the rationale of MS1-based strategies and then important considerations for experimental and data processing techniques, with the emphasis on (i) efficient and reproducible sample preparation and LC separation; (ii) sensitive, selective and high-resolution MS detection; iii)accurate chromatographic alignment; (iv) sensitive and selective generation of quantitative features; and (v) optimal post-feature-generation data quality control. Prominent technical developments in these aspects are discussed. Finally, we reviewed applications of MS1-based strategy in disease mechanism studies, biomarker discovery, and pharmaceutical investigations.
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Affiliation(s)
- Xue Wang
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloNew York
| | - Shichen Shen
- Department of Pharmaceutical SciencesUniversity at BuffaloState University of New YorkNew YorkNew York
| | - Sailee Suryakant Rasam
- Department of Biochemistry, University at BuffaloState University of New YorkNew YorkNew York
| | - Jun Qu
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloNew York
- Department of Pharmaceutical SciencesUniversity at BuffaloState University of New YorkNew YorkNew York
- Department of Biochemistry, University at BuffaloState University of New YorkNew YorkNew York
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