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Cui Y, Wang X, Xu J, Liu X, Wang X, Pang J, Song Y, Yu M, Song W, Luo X, Liu M, Sun S. PROTEOMIC ANALYSIS OF TAENIA SOLIUM CYST FLUID BY SHOTGUN LC-MS/MS. J Parasitol 2021; 107:799-809. [PMID: 34648630 DOI: 10.1645/20-65] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Taenia solium cysts were collected from pig skeletal muscle and analyzed via a shotgun proteomic approach to identify known proteins in the cyst fluid and to explore host-parasite interactions. Cyst fluid was aseptically collected and analyzed with shotgun liquid chromatography-tandem mass spectrometry (LC-MS/MS). Gene alignment and annotation were performed using Blast2GO software followed by gene ontology analysis of the annotated proteins. The pathways were further analyzed with the Kyoto Encyclopedia of Genes and Genomes (KEGG), and a protein-protein interaction (PPI) network map was generated using STRING software. A total of 158 known proteins were identified, most of which were low-molecular-mass proteins. These proteins were mainly involved in cellular and metabolic processes, and their molecular functions were predominantly related to catalytic activity and binding functions. The pathway enrichment analysis revealed that the known proteins were mainly enriched in the PI3K-Akt and glycolysis/gluconeogenesis signaling pathways. The nodes in the PPI network mainly consisted of enzymes involved in sugar metabolism. The cyst fluid proteins screened in this study may play important roles in the interaction between the cysticerci and the host. The shotgun LC-MS/MS, gene ontology, KEGG, and PPI network map data will be used to identify and analyze the cyst fluid proteome of cysticerci, which will provide a basis for further exploration of the invasion and activities of T. solium.
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Affiliation(s)
- Yaxuan Cui
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Inner Mongolia Tongliao 028042, China
| | - Xinrui Wang
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Inner Mongolia Tongliao 028042, China
| | - Jing Xu
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Inner Mongolia Tongliao 028042, China
| | - Xiaolei Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis/College of Veterinary Medicine, Jilin University, Changchun 130000, China
| | - Xuelin Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis/College of Veterinary Medicine, Jilin University, Changchun 130000, China
| | - Jianda Pang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis/College of Veterinary Medicine, Jilin University, Changchun 130000, China
| | - Yining Song
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Inner Mongolia Tongliao 028042, China
| | - Mingchuan Yu
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Inner Mongolia Tongliao 028042, China
| | - Weiyi Song
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Inner Mongolia Tongliao 028042, China
| | - Xuenong Luo
- Key Laboratory of Veterinary Parasitology of Gansu Province, State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Mingyuan Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis/College of Veterinary Medicine, Jilin University, Changchun 130000, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225000, China
| | - Shumin Sun
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Inner Mongolia Tongliao 028042, China.,College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
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2
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Assessment of sample preparation methods for metaproteomics of extracellular proteins. Anal Biochem 2017; 516:23-36. [DOI: 10.1016/j.ab.2016.10.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/06/2016] [Accepted: 10/08/2016] [Indexed: 02/01/2023]
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3
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Fujioka H, Sakai A, Tanaka S, Kimura K, Miyamoto A, Iwamoto M, Uchiyama K. Comparative proteomic analysis of paclitaxel resistance-related proteins in human breast cancer cell lines. Oncol Lett 2016; 13:289-295. [PMID: 28123557 DOI: 10.3892/ol.2016.5455] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 10/06/2016] [Indexed: 11/06/2022] Open
Abstract
Paclitaxel is widely used to treat various cancers; however, resistance to this drug is a major obstacle to breast cancer chemotherapy. To identify the proteins involved in paclitaxel resistance, the present study compared the proteomes of MCF-7 human breast cancer cells and its paclitaxel-resistant subclone MCF-7/PTX. Using two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time of flight mass spectrometry, 11 upregulated and 12 downregulated proteins were identified in MCF-7/PTX cells compared with the parental cell line. These 23 proteins were functionally classified as stress-induced chaperones, metabolic enzymes and cytoskeletal proteins. The anti-apoptotic proteins, stress-70 protein, 78-kD glucose-regulated protein, peptidyl-prolyl cis-trans isomerase A (PPIA) and heterogeneous nuclear ribonucleoprotein H3, were also upregulated in MCF-7/PTX cells. Notably, knockdown of the stress-response chaperone PPIA using small interfering RNA in MCF-7/PTX cells restored their sensitivity to paclitaxel. These findings indicated that PPIA may have an important role in paclitaxel resistance in MCF-7/PTX cells.
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Affiliation(s)
- Hiroya Fujioka
- Section of Breast and Endocrine Surgery, Department of General and Gastroenterological Surgery, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
| | - Akiko Sakai
- Department of Chemistry, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
| | - Satoru Tanaka
- Section of Breast and Endocrine Surgery, Department of General and Gastroenterological Surgery, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
| | - Kosei Kimura
- Section of Breast and Endocrine Surgery, Department of General and Gastroenterological Surgery, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
| | - Akiko Miyamoto
- Section of Breast and Endocrine Surgery, Department of General and Gastroenterological Surgery, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
| | - Mitsuhiko Iwamoto
- Section of Breast and Endocrine Surgery, Department of General and Gastroenterological Surgery, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
| | - Kazuhisa Uchiyama
- Section of Breast and Endocrine Surgery, Department of General and Gastroenterological Surgery, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
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Guerreiro JF, Sampaio-Marques B, Soares R, Coelho AV, Leão C, Ludovico P, Sá-Correia I. Mitochondrial proteomics of the acetic acid - induced programmed cell death response in a highly tolerant Zygosaccharomyces bailii - derived hybrid strain. MICROBIAL CELL 2016; 3:65-78. [PMID: 28357336 PMCID: PMC5349105 DOI: 10.15698/mic2016.02.477] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Very high concentrations of acetic acid at low pH induce programmed cell death
(PCD) in both the experimental model Saccharomyces cerevisiae
and in Zygosaccharomyces bailii, the latter being considered
the most problematic acidic food spoilage yeast due to its remarkable intrinsic
resistance to this food preservative. However, while the mechanisms underlying
S. cerevisiae PCD induced by acetic acid have been
previously examined, the corresponding molecular players remain largely unknown
in Z. bailii. Also, the reason why acetic acid concentrations
known to be necrotic for S. cerevisiae induce PCD with an
apoptotic phenotype in Z. bailii remains to be elucidated. In
this study, a 2-DE-based expression mitochondrial proteomic analysis was
explored to obtain new insights into the mechanisms involved in PCD in the
Z. bailii derived hybrid strain ISA1307. This allowed the
quantitative assessment of expression of protein species derived from each of
the parental strains, with special emphasis on the processes taking place in the
mitochondria known to play a key role in acetic acid - induced PCD. A marked
decrease in the content of proteins involved in mitochondrial metabolism, in
particular, in respiratory metabolism (Cor1, Rip1, Lpd1, Lat1 and Pdb1), with a
concomitant increase in the abundance of proteins involved in fermentation
(Pdc1, Ald4, Dld3) was registered. Other differentially expressed identified
proteins also suggest the involvement of the oxidative stress response, protein
translation, amino acid and nucleotide metabolism, among other processes, in the
PCD response. Overall, the results strengthen the emerging concept of the
importance of metabolic regulation of yeast PCD.
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Affiliation(s)
- Joana F Guerreiro
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - Belém Sampaio-Marques
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga 4710-057, Portugal. ; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Renata Soares
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Ana V Coelho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Cecília Leão
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga 4710-057, Portugal. ; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Paula Ludovico
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga 4710-057, Portugal. ; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
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Walsh G. Proteins and Proteomics. Proteins 2015. [DOI: 10.1002/9781119117599.ch1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Lee JJ, Simborio HL, Reyes AWB, Kim DG, Hop HT, Min W, Her M, Jung SC, Yoo HS, Kim S. Proteomic analyses of the time course responses of mice infected with Brucella abortus 544 reveal immunogenic antigens. FEMS Microbiol Lett 2014; 357:164-74. [PMID: 24975114 DOI: 10.1111/1574-6968.12522] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 06/02/2014] [Accepted: 06/18/2014] [Indexed: 11/28/2022] Open
Abstract
Brucellosis is a major zoonotic disease caused by pathogens of the genus Brucella. The eradication of brucellosis in domestic animals, associated with the prevention of human infection, can be attained through accurate diagnosis. However, the conventional serological diagnosis of brucellosis has limitations, particularly in detecting the infection period. Accordingly, the aim of this study was to determine reliable immunogenic proteins to detect Brucella abortus infection according to time course responses to aid in the appropriate management of this disease. Proteomic identification through two-dimensional electrophoresis (2DE), followed by immunoblotting, revealed 13, 24, and 55 immunodominant B. abortus 544 proteins that were reactive to sera from experimentally infected mice at early (10 days), middle (30 days), and late (60 days) infection periods, respectively. After excluding several spots reactive to sera from Yersinia enterocolitica O:9-infected and noninfected mice, 17 of the 67 immunodominant proteins were identified through MALDI-TOF MS. Consequently, the identified proteins showed time course-dependent immunogenicity against Brucella infection. Thus, the results of this study suggest that the production of immunogenic proteins during infection periods improves the diagnosis and discovery of vaccine candidates.
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Affiliation(s)
- Jin Ju Lee
- Animal and Plant Quarantine Agency, Anyang, Gyeonggi-do, Korea
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7
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Proteome studies of bacterial antibiotic resistance mechanisms. J Proteomics 2014; 97:88-99. [DOI: 10.1016/j.jprot.2013.10.027] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 10/12/2013] [Accepted: 10/19/2013] [Indexed: 01/10/2023]
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8
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Fowsantear W, Argo E, Pattinson C, Cash P. Comparative proteomics of Helicobacter species: the discrimination of gastric and enterohepatic Helicobacter species. J Proteomics 2013; 97:245-55. [PMID: 23899588 DOI: 10.1016/j.jprot.2013.07.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 07/11/2013] [Accepted: 07/14/2013] [Indexed: 12/26/2022]
Abstract
UNLABELLED Helicobacter pylori is a major human pathogen that infects the gastric mucosa and is responsible for a range of infections including gastritis and gastric carcinoma. Although other bacteria within the Helicobacter genus can also infect the gastric mucosa, there are Helicobacter species that infect alternative sites within the gastrointestinal (GI) tract. Two-dimensional gel electrophoresis was used to compare the cellular proteomes of seven non-pylori Helicobacters (H. mustelae, H. felis, H. cinaedi, H. hepaticus, H. fennelliae, H. bilis and H. cholecystus) against the more extensively characterised H. pylori. The different Helicobacter species showed distinctive 2D protein profiles, it was possible to combine them into a single dataset using Progenesis SameSpots software. Principal Component Analysis was used to search for correlations between the bacterial proteomes and their sites of infection. This approach clearly discriminated between gastric (i.e. those which infect in the gastric mucosa) and enterohepatic Helicobacter species (i.e. those bacteria that infect the small intestine and hepatobillary regions of the GI tract). Selected protein spots showing significant differences in abundance between these two groups of bacteria were identified by LC-MS. The data provide an initial insight into defining those features of the bacterial proteome that influence the sites of bacterial infection. BIOLOGICAL SIGNIFICANCE This study demonstrated that representative members of the Helicobacter genus were readily discriminated from each other on the basis of their in vitro whole cell proteomes determined using 2D gel electrophoresis. Despite the intra-species heterogeneity observed it was possible, to demonstrate that the enterohepatic (represented by H. bilis, H. hepaticus, H. fennelliae, H. cinaedi and H. cholecystus) and gastric (represented by H. pylori, H. mustelae, and H. felis) Helicobacters formed discrete groups based on their 2D protein profiles. A provisional proteomic signature was identified that correlated with the typical sites of colonisation of these members of the Helicobacter genus. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- Winita Fowsantear
- Division of Applied Medicine, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom
| | - Evelyn Argo
- Division of Applied Medicine, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom
| | - Craig Pattinson
- Division of Applied Medicine, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom
| | - Phillip Cash
- Division of Applied Medicine, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom.
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9
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Identification of HSP90 as potential biomarker of biliary atresia using two-dimensional electrophoresis and mass spectrometry. PLoS One 2013; 8:e68602. [PMID: 23874684 PMCID: PMC3708914 DOI: 10.1371/journal.pone.0068602] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Accepted: 05/31/2013] [Indexed: 12/26/2022] Open
Abstract
Biliary atresia (BA) is a devastating cholestatic liver disease targeting infants. Current diagnosis depends on surgical exploration of the biliary tree. The aim of the present study was to identify potential biomarkers for the diagnosis of biliary atresia (BA). Two-dimensional electrophoresis was utilized for the identification of proteins that were differentially expressed in liver biopsies of 20 BA patients and 12 infants with non-BA neonatal cholestasis (NC) as controls. Using mass spectrometry, we identified 15 proteins with expressions significantly altered. Out of the 15 proteins identified, heat shock protein (HSP) 90 was the most significantly altered and was down-regulated in BA samples compared to NC samples using immunoblotting analysis. Our findings suggest that HSP90 might be a potential biomarker for the diagnosis of BA and may be used for monitoring further development and therapy for BA. This study demonstrated that a comprehensive strategy of proteomic identification combined with further validation should be adopted in biomarker discovery.
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10
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Guerreiro JF, Mira NP, Sá-Correia I. Adaptive response to acetic acid in the highly resistant yeast species Zygosaccharomyces bailii revealed by quantitative proteomics. Proteomics 2013; 12:2303-18. [PMID: 22685079 DOI: 10.1002/pmic.201100457] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Zygosaccharomyces bailii is the most tolerant yeast species to acetic acid-induced toxicity, being able to grow in the presence of concentrations of this food preservative close to the legal limits. For this reason, Z. bailii is the most important microbial contaminant of acidic food products but the mechanisms behind this intrinsic resistance to acetic acid are very poorly characterized. To gain insights into the adaptive response and tolerance to acetic acid in Z. bailii, we explored an expression proteomics approach, based on quantitative 2DE, to identify alterations occurring in the protein content in response to sudden exposure or balanced growth in the presence of an inhibitory but nonlethal concentration of this weak acid. A coordinate increase in the content of proteins involved in cellular metabolism, in particular, in carbohydrate metabolism (Mdh1p, Aco1p, Cit1p, Idh2p, and Lpd1p) and energy generation (Atp1p and Atp2p), as well as in general and oxidative stress response (Sod2p, Dak2p, Omp2p) was registered. Results reinforce the concept that glucose and acetic acid are coconsumed in Z. bailii, with acetate being channeled into the tricarboxylic acid cycle. When acetic acid is the sole carbon source, results suggest the activation of gluconeogenic and pentose phosphate pathways, based on the increased content of several proteins of these pathways after glucose exhaustion.
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Affiliation(s)
- Joana F Guerreiro
- Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Department of Bioengineering, Instituto Superior Técnico, Technical University of Lisbon, Portugal
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11
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Vranakis I, Papadioti A, Tselentis Y, Psaroulaki A, Tsiotis G. The contribution of proteomics towards deciphering the enigma ofCoxiella burnetii. Proteomics Clin Appl 2013; 7:193-204. [DOI: 10.1002/prca.201200096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 11/15/2012] [Accepted: 11/20/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Iosif Vranakis
- Regional Laboratory of Public Health of Crete; Heraklion; Greece
| | - Anastasia Papadioti
- Division of Biochemistry; Department of Chemistry; University of Crete; Voutes; Greece
| | - Yannis Tselentis
- Regional Laboratory of Public Health of Crete; Heraklion; Greece
| | | | - Georgios Tsiotis
- Division of Biochemistry; Department of Chemistry; University of Crete; Voutes; Greece
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12
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Higashisaka K, Yoshioka Y, Yamashita K, Morishita Y, Pan H, Ogura T, Nagano T, Kunieda A, Nagano K, Abe Y, Kamada H, Tsunoda SI, Nabeshi H, Yoshikawa T, Tsutsumi Y. Hemopexin as biomarkers for analyzing the biological responses associated with exposure to silica nanoparticles. NANOSCALE RESEARCH LETTERS 2012; 7:555. [PMID: 23039107 PMCID: PMC3487985 DOI: 10.1186/1556-276x-7-555] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 09/21/2012] [Indexed: 05/10/2023]
Abstract
Practical uses of nanomaterials are rapidly spreading to a wide variety of fields. However, potential harmful effects of nanomaterials are raising concerns about their safety. Therefore, it is important that a risk assessment system is developed so that the safety of nanomaterials can be evaluated or predicted. Here, we attempted to identify novel biomarkers of nanomaterial-induced health effects by a comprehensive screen of plasma proteins using two-dimensional differential in gel electrophoresis (2D-DIGE) analysis. Initially, we used 2D-DIGE to analyze changes in the level of plasma proteins in mice after intravenous injection via tail veins of 0.8 mg/mouse silica nanoparticles with diameters of 70 nm (nSP70) or saline as controls. By quantitative image analysis, protein spots representing >2.0-fold alteration in expression were found and identified by mass spectrometry. Among these proteins, we focused on hemopexin as a potential biomarker. The levels of hemopexin in the plasma increased as the silica particle size decreased. In addition, the production of hemopexin depended on the characteristics of the nanomaterials. These results suggested that hemopexin could be an additional biomarker for analyzing the biological responses associated with exposure to silica nanoparticles. We believe that this study will contribute to the development of biomarkers to ensure the safety of silica nanoparticles.
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Affiliation(s)
- Kazuma Higashisaka
- Laboratory of Toxicology and Safety Science, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yasuo Yoshioka
- Laboratory of Toxicology and Safety Science, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kohei Yamashita
- Laboratory of Toxicology and Safety Science, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuki Morishita
- Laboratory of Toxicology and Safety Science, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Huiyan Pan
- Laboratory of Toxicology and Safety Science, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Toshinobu Ogura
- Laboratory of Toxicology and Safety Science, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takashi Nagano
- Laboratory of Toxicology and Safety Science, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Akiyoshi Kunieda
- Laboratory of Toxicology and Safety Science, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kazuya Nagano
- Laboratory of Biopharmaceutical Research, National Institute of Biomedical Innovation, 7-6-8, Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
| | - Yasuhiro Abe
- Cancer Biology Research Center, Sanford Research/USD, 2301 E. 60th Street N, Sioux Falls, SD, 57104, USA
| | - Haruhiko Kamada
- Laboratory of Biopharmaceutical Research, National Institute of Biomedical Innovation, 7-6-8, Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
- The Center for Advanced Medical Engineering and Informatics, Osaka University, 1-6, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shin-ichi Tsunoda
- Laboratory of Biopharmaceutical Research, National Institute of Biomedical Innovation, 7-6-8, Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
- The Center for Advanced Medical Engineering and Informatics, Osaka University, 1-6, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hiromi Nabeshi
- Division of Foods, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501, Japan
| | - Tomoaki Yoshikawa
- Laboratory of Toxicology and Safety Science, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yasuo Tsutsumi
- Laboratory of Toxicology and Safety Science, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Laboratory of Biopharmaceutical Research, National Institute of Biomedical Innovation, 7-6-8, Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
- The Center for Advanced Medical Engineering and Informatics, Osaka University, 1-6, Yamadaoka, Suita, Osaka, 565-0871, Japan
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Madeira A, da Silva CL, dos Santos F, Camafeita E, Cabral JMS, Sá-Correia I. Human mesenchymal stem cell expression program upon extended ex-vivo cultivation, as revealed by 2-DE-based quantitative proteomics. PLoS One 2012; 7:e43523. [PMID: 22916271 PMCID: PMC3423346 DOI: 10.1371/journal.pone.0043523] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 07/23/2012] [Indexed: 12/31/2022] Open
Abstract
Human mesenchymal stem cells (MSC) have been on the focus of intense clinical-oriented research due to their multilineage differentiation potential and immunomodulatory properties. However, to reach the clinically meaningful cell numbers for cellular therapy and tissue engineering applications, MSC ex-vivo expansion is mandatory but sequential cell passaging results in loss of proliferative, clonogenic and differentiation potential. To get clues into the molecular mechanisms underlying cellular senescence resulting from extended ex-vivo cultivation of bone marrow (BM) MSC, we explored a two-dimensional gel electrophoresis (2-DE) based quantitative proteomics to compare the expression programs of Passage 3 cells (P3), commonly used in clinical studies with expanded MSC, and Passage 7 (P7) cells, which already demonstrated significant signs of culture-induced senescence. Proteins of the functional categories "Structural components and cellular cytoskeleton" and "Folding and stress response proteins" are less abundant in P7 cells, compared to P3, while proteins involved in "Energy metabolism", "Cell cycle regulation and aging" and "Apoptosis" are more abundant. The large number of multiple size and charge isoforms with an altered content that were identified in this study in P7 versus P3, namely the cytoskeleton components β-actin (7 forms) and vimentin (24 forms), also emphasizes the importance of post-transcriptional modification upon long-term cultivation. The differential protein expression registered suggests that cellular senescence occurring during ex-vivo expansion of BM MSC is associated with the impairment of cytoskeleton remodeling and/or organization and the repair of damaged proteins resulting from cell exposure to culture stress. The genome-wide expression approach used in this study has proven useful for getting mechanistic insights into the observed decrease on the proliferative and clonogenic potential of P7 versus P3 cells and paves the way to set up a proteome profiling strategy for quality control to assure safe and clinically effective expanded MSC.
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Affiliation(s)
- Andreia Madeira
- Institute for Biotechnology and Bioengineering (IBB), Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Lisboa, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Technical University of Lisbon, Lisboa, Portugal
| | - Cláudia L. da Silva
- Institute for Biotechnology and Bioengineering (IBB), Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Lisboa, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Technical University of Lisbon, Lisboa, Portugal
| | - Francisco dos Santos
- Institute for Biotechnology and Bioengineering (IBB), Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Lisboa, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Technical University of Lisbon, Lisboa, Portugal
| | - Emilio Camafeita
- Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares, CNIC, Melchor Fernández Almagro 3, Madrid, Spain
| | - Joaquim M. S. Cabral
- Institute for Biotechnology and Bioengineering (IBB), Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Lisboa, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Technical University of Lisbon, Lisboa, Portugal
| | - Isabel Sá-Correia
- Institute for Biotechnology and Bioengineering (IBB), Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Lisboa, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Technical University of Lisbon, Lisboa, Portugal
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Mass spectrometry and animal science: Protein identification strategies and particularities of farm animal species. J Proteomics 2012; 75:4190-206. [DOI: 10.1016/j.jprot.2012.04.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 03/17/2012] [Accepted: 04/08/2012] [Indexed: 12/30/2022]
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15
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Dos Santos SC, Teixeira MC, Cabrito TR, Sá-Correia I. Yeast toxicogenomics: genome-wide responses to chemical stresses with impact in environmental health, pharmacology, and biotechnology. Front Genet 2012; 3:63. [PMID: 22529852 PMCID: PMC3329712 DOI: 10.3389/fgene.2012.00063] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 04/03/2012] [Indexed: 01/20/2023] Open
Abstract
The emerging transdisciplinary field of Toxicogenomics aims to study the cell response to a given toxicant at the genome, transcriptome, proteome, and metabolome levels. This approach is expected to provide earlier and more sensitive biomarkers of toxicological responses and help in the delineation of regulatory risk assessment. The use of model organisms to gather such genomic information, through the exploitation of Omics and Bioinformatics approaches and tools, together with more focused molecular and cellular biology studies are rapidly increasing our understanding and providing an integrative view on how cells interact with their environment. The use of the model eukaryote Saccharomyces cerevisiae in the field of Toxicogenomics is discussed in this review. Despite the limitations intrinsic to the use of such a simple single cell experimental model, S. cerevisiae appears to be very useful as a first screening tool, limiting the use of animal models. Moreover, it is also one of the most interesting systems to obtain a truly global understanding of the toxicological response and resistance mechanisms, being in the frontline of systems biology research and developments. The impact of the knowledge gathered in the yeast model, through the use of Toxicogenomics approaches, is highlighted here by its use in prediction of toxicological outcomes of exposure to pesticides and pharmaceutical drugs, but also by its impact in biotechnology, namely in the development of more robust crops and in the improvement of yeast strains as cell factories.
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Affiliation(s)
- Sandra C Dos Santos
- Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Technical University of Lisbon Lisbon, Portugal
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Oliveira AP, Sauer U. The importance of post-translational modifications in regulating Saccharomyces cerevisiae metabolism. FEMS Yeast Res 2011; 12:104-17. [DOI: 10.1111/j.1567-1364.2011.00765.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 11/22/2011] [Accepted: 11/23/2011] [Indexed: 11/30/2022] Open
Affiliation(s)
- Ana Paula Oliveira
- Institute of Molecular Systems Biology; Department of Biology; ETH Zurich; Zurich; Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology; Department of Biology; ETH Zurich; Zurich; Switzerland
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Hartson SD, Matts RL. Approaches for defining the Hsp90-dependent proteome. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1823:656-67. [PMID: 21906632 DOI: 10.1016/j.bbamcr.2011.08.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 08/22/2011] [Accepted: 08/23/2011] [Indexed: 10/17/2022]
Abstract
Hsp90 is the target of ongoing drug discovery studies seeking new compounds to treat cancer, neurodegenerative diseases, and protein folding disorders. To better understand Hsp90's roles in cellular pathologies and in normal cells, numerous studies have utilized proteomics assays and related high-throughput tools to characterize its physical and functional protein partnerships. This review surveys these studies, and summarizes the strengths and limitations of the individual attacks. We also include downloadable spreadsheets compiling all of the Hsp90-interacting proteins identified in more than 23 studies. These tools include cross-references among gene aliases, human homologues of yeast Hsp90-interacting proteins, hyperlinks to database entries, summaries of canonical pathways that are enriched in the Hsp90 interactome, and additional bioinformatic annotations. In addition to summarizing Hsp90 proteomics studies performed to date and the insights they have provided, we identify gaps in our current understanding of Hsp90-mediated proteostasis. This article is part of a Special Issue entitled: Heat Shock Protein 90 (HSP90).
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Affiliation(s)
- Steven D Hartson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA
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18
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Alberghina L, Mavelli G, Drovandi G, Palumbo P, Pessina S, Tripodi F, Coccetti P, Vanoni M. Cell growth and cell cycle in Saccharomyces cerevisiae: basic regulatory design and protein-protein interaction network. Biotechnol Adv 2011; 30:52-72. [PMID: 21821114 DOI: 10.1016/j.biotechadv.2011.07.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 06/23/2011] [Accepted: 07/06/2011] [Indexed: 10/18/2022]
Abstract
In this review we summarize the major connections between cell growth and cell cycle in the model eukaryote Saccharomyces cerevisiae. In S. cerevisiae regulation of cell cycle progression is achieved predominantly during a narrow interval in the late G1 phase known as START (Pringle and Hartwell, 1981). At START a yeast cell integrates environmental and internal signals (such as nutrient availability, presence of pheromone, attainment of a critical size, status of the metabolic machinery) and decides whether to enter a new cell cycle or to undertake an alternative developmental program. Several signaling pathways, that act to connect the nutritional status to cellular actions, are briefly outlined. A Growth & Cycle interaction network has been manually curated. More than one fifth of the edges within the Growth & Cycle network connect Growth and Cycle proteins, indicating a strong interconnection between the processes of cell growth and cell cycle. The backbone of the Growth & Cycle network is composed of middle-degree nodes suggesting that it shares some properties with HOT networks. The development of multi-scale modeling and simulation analysis will help to elucidate relevant central features of growth and cycle as well as to identify their system-level properties. Confident collaborative efforts involving different expertises will allow to construct consensus, integrated models effectively linking the processes of cell growth and cell cycle, ultimately contributing to shed more light also on diseases in which an altered proliferation ability is observed, such as cancer.
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Affiliation(s)
- Lilia Alberghina
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy.
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