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Kilic P, Karabudak S, Cosar B, Savran BN, Yalcin M. Residual protein analysis by SDS-PAGE in clinically manufactured BM-MSC products. Electrophoresis 2024. [PMID: 38687192 DOI: 10.1002/elps.202300286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 05/02/2024]
Abstract
Residual substances that are considered hazardous to the recipient must be removed from final cellular therapeutic products manufactured for clinical purposes. In doing so, quality rules determined by competent authorities (CAs) for the clinical use of tissue- and cell-based products can be met. In our study, we carried out residual substance analyses, and purity determination studies of trypsin and trypsin inhibitor in clinically manufactured bone marrow-derived mesenchymal stromal/stem cell products, using the sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) method. Despite being a semiquantitative method, SDS-PAGE has several benefits over other methods for protein analysis, such as simplicity, convenience of use, and affordability. Due to its convenience and adaptability, SDS-PAGE is still a commonly used method in many laboratories, despite its limits in dynamic range and quantitative precision. Our goal in this work was to show that SDS-PAGE may be used effectively for protein measurement, especially where practicality and affordability are the major factors. The results of our study suggest a validated method to guide tissue and cell manufacturing sites for making use of an agreeable, accessible, and cost-effective method for residual substance analyses in clinically manufactured cellular therapies.
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Affiliation(s)
- Pelin Kilic
- Department of Stem Cells and Regenerative Medicine, Stem Cell Institute, Ankara University, Ankara, Turkey
- HücreCELL® Biotechnology Development and Commerce, Inc., Ankara, Turkey
| | - Sema Karabudak
- Department of Medical Genetics, Medical Faculty, Ankara Yıldırım Beyazıt University, Ankara, Turkey
- Central Research Laboratory Research and Application Center, Ankara Yıldırım Beyazıt University, Ankara, Turkey
| | - Begum Cosar
- HücreCELL® Biotechnology Development and Commerce, Inc., Ankara, Turkey
- Department of Molecular Biology and Genetics, Institute of Science, Başkent University, Ankara, Turkey
| | - Busra Nigar Savran
- HücreCELL® Biotechnology Development and Commerce, Inc., Ankara, Turkey
- Department of Biology, Middle East Technical University, Ankara, Turkey
| | - Merve Yalcin
- School of Pharmacy English Program, Ankara University, Ankara, Turkey
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Rekstina VV, Sabirzyanova TA, Sabirzyanov FA, Adzhubei AA, Tkachev YV, Kudryashova IB, Snalina NE, Bykova AA, Alessenko AV, Ziganshin RH, Kuznetsov SA, Kalebina TS. The Post-Translational Modifications, Localization, and Mode of Attachment of Non-Covalently Bound Glucanosyltransglycosylases of Yeast Cell Wall as a Key to Understanding their Functioning. Int J Mol Sci 2020; 21:ijms21218304. [PMID: 33167499 PMCID: PMC7663962 DOI: 10.3390/ijms21218304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/26/2020] [Accepted: 10/30/2020] [Indexed: 01/27/2023] Open
Abstract
Glucan linked to proteins is a natural mega-glycoconjugate (mGC) playing the central role as a structural component of a yeast cell wall (CW). Regulation of functioning of non-covalently bound glucanosyltransglycosylases (ncGTGs) that have to remodel mGC to provide CW extension is poorly understood. We demonstrate that the main ncGTGs Bgl2 and Scw4 have phosphorylated and glutathionylated residues and are represented in CW as different pools of molecules having various firmness of attachment. Identified pools contain Bgl2 molecules with unmodified peptides, but differ from each other in the presence and combination of modified ones, as well as in the presence or absence of other CW proteins. Correlation of Bgl2 distribution among pools and its N-glycosylation was not found. Glutathione affects Bgl2 conformation, probably resulting in the mode of its attachment and enzymatic activity. Bgl2 from the pool of unmodified and monophosphorylated molecules demonstrates the ability to fibrillate after isolation from CW. Revealing of Bgl2 microcompartments and their mosaic arrangement summarized with the results obtained give the evidence that the functioning of ncGTGs in CW can be controlled by reversible post-translational modifications and facilitated due to their compact localization. The hypothetical scheme of distribution of Bgl2 inside CW is represented.
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Affiliation(s)
- Valentina V. Rekstina
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (V.V.R.); (T.A.S.); (F.A.S.); (I.B.K.); (A.A.B.)
| | - Tatyana A. Sabirzyanova
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (V.V.R.); (T.A.S.); (F.A.S.); (I.B.K.); (A.A.B.)
| | - Fanis A. Sabirzyanov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (V.V.R.); (T.A.S.); (F.A.S.); (I.B.K.); (A.A.B.)
| | - Alexei A. Adzhubei
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (A.A.A.); (Y.V.T.)
| | - Yaroslav V. Tkachev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (A.A.A.); (Y.V.T.)
| | - Irina B. Kudryashova
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (V.V.R.); (T.A.S.); (F.A.S.); (I.B.K.); (A.A.B.)
| | - Natalia E. Snalina
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia; (N.E.S.); (A.V.A.)
| | - Anastasia A. Bykova
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (V.V.R.); (T.A.S.); (F.A.S.); (I.B.K.); (A.A.B.)
| | - Alice V. Alessenko
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia; (N.E.S.); (A.V.A.)
| | - Rustam H. Ziganshin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia;
| | - Sergei A. Kuznetsov
- Institute of Biological Sciences, University of Rostock, 18059 Rostock, Germany;
| | - Tatyana S. Kalebina
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (V.V.R.); (T.A.S.); (F.A.S.); (I.B.K.); (A.A.B.)
- Correspondence: ; Tel.: +7-(495)-939-50-75
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Novoa-Herran S, Umaña-Perez A, Canals F, Sanchez-Gomez M. Serum depletion induces changes in protein expression in the trophoblast-derived cell line HTR-8/SVneo. Cell Mol Biol Lett 2016; 21:22. [PMID: 28536624 PMCID: PMC5415790 DOI: 10.1186/s11658-016-0018-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 07/05/2016] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND How nutrition and growth factor restriction due to serum depletion affect trophoblast function remains poorly understood. We performed a proteomic differential study of the effects of serum depletion on a first trimester human immortalized trophoblast cell line. METHODS The viability of HTR-8/SVneo trophoblast cells in culture with 0, 0.5 and 10 % fetal bovine serum (FBS) were assayed via MTT at 24, 48 and 64 h. A comparative proteomic analysis of the cells grown with those FBS levels for 24 h was performed using two-dimensional electrophoresis (2DE), followed by mass spectrometry for protein spot identification, and a database search and bioinformatics analysis of the expressed proteins. Differential spots were identified using the Kolmogorov-Smirnov test (n = 3, significance level 0.10, D > 0.642) and/or ANOVA (n = 3, p < 0.05). RESULTS The results showed that low serum doses or serum depletion differentially affect cell growth and protein expression. Differential expression was seen in 25 % of the protein spots grown with 0.5 % FBS and in 84 % of those grown with 0 % FBS, using 10 % serum as the physiological control. In 0.5 % FBS, this difference was related with biological processes typically affected by the serum, such as cell cycle, regulation of apoptosis and proliferation. In addition to these changes, in the serum-depleted proteome we observed downregulation of keratin 8, and upregulation of vimentin, the glycolytic enzymes enolase and pyruvate kinase (PKM2) and tumor progression-related inosine-5'-monophosphate dehydrogenase 2 (IMPDH2) enzyme. The proteins regulated by total serum depletion, but not affected by growth in 0.5 % serum, are members of the glycolytic and nucleotide metabolic pathways and the epithelial-to-mesenchymal transition (EMT), suggesting an adaptive switch characteristic of malignant cells. CONCLUSIONS This comparative proteomic analysis and the identified proteins are the first evidence of a protein expression response to serum depletion in a trophoblast cell model. Our results show that serum depletion induces specific changes in protein expression concordant with main cell metabolic adaptations and EMT, resembling the progression to a malignant phenotype.
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Affiliation(s)
- Susana Novoa-Herran
- Departamento de Química, Grupo de Investigación en Hormonas (Hormone Research Laboratory), Universidad Nacional de Colombia, Sede Bogotá, Facultad de Ciencias, Cra 30 45-03 Ed 451 Of 464, AA 111321 Bogotá, Colombia
| | - Adriana Umaña-Perez
- Departamento de Química, Grupo de Investigación en Hormonas (Hormone Research Laboratory), Universidad Nacional de Colombia, Sede Bogotá, Facultad de Ciencias, Cra 30 45-03 Ed 451 Of 464, AA 111321 Bogotá, Colombia
| | - Francesc Canals
- Laboratory of Proteomics, Vall d'Hebron Institute of Oncology (VHIO), Centre Cellex, C Natzaret 115-117, 08035 Barcelona, Spain
| | - Myriam Sanchez-Gomez
- Departamento de Química, Grupo de Investigación en Hormonas (Hormone Research Laboratory), Universidad Nacional de Colombia, Sede Bogotá, Facultad de Ciencias, Cra 30 45-03 Ed 451 Of 464, AA 111321 Bogotá, Colombia
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Zhao S, Zhao X, Zou H, Fu J, Du G, Zhou J, Chen J. Comparative proteomic analysis of Saccharomyces cerevisiae under different nitrogen sources. J Proteomics 2014; 101:102-12. [PMID: 24530623 DOI: 10.1016/j.jprot.2014.01.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Revised: 11/28/2013] [Accepted: 01/24/2014] [Indexed: 11/15/2022]
Abstract
In cultures containing multiple sources of nitrogen, Saccharomyces cerevisiae exhibits a sequential use of nitrogen sources through a mechanism known as nitrogen catabolite repression (NCR). To identify proteins differentially expressed due to NCR, proteomic analysis of S. cerevisiae S288C under different nitrogen source conditions was performed using two-dimensional gel electrophoresis (2-DE), revealing 169 candidate protein spots. Among these 169 protein spots, 121 were identified by matrix assisted laser desorption ionization-time of flight/time of flight mass spectrometry (MALDI-TOF/TOF). The identified proteins were closely associated with four main biological processes through Gene Ontology (GO) categorical analysis. The identification of the potential proteins and cellular processes related to NCR offer a global overview of changes elicited by different nitrogen sources, providing clues into how yeast adapt to different nutritional conditions. Moreover, by comparing our proteomic data with corresponding mRNA data, proteins regulated at the transcriptional and post-transcriptional level could be distinguished. Biological significance In S. cerevisiae, different nitrogen sources provide different growth characteristics and generate different metabolites. The nitrogen catabolite repression (NCR) process plays an important role for S. cerevisiae in the ordinal utilization of different nitrogen sources. NCR process can result in significant shift of global metabolic networks. Previous works on NCR primarily focused on transcriptomic level. The results obtained in this study provided a global atlas of the proteome changes triggered by different nitrogen sources and would facilitate the understanding of mechanisms for how yeast could adapt to different nutritional conditions.
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Affiliation(s)
- Shaohui Zhao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Xinrui Zhao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Huijun Zou
- Zhejiang Guyuelongshan Shaoxing Wine Company, 13 Yangjiang Road, Shaoxing, Zhejiang 312000, China
| | - Jianwei Fu
- Zhejiang Guyuelongshan Shaoxing Wine Company, 13 Yangjiang Road, Shaoxing, Zhejiang 312000, China
| | - Guocheng Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Jian Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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Abbaraju NV, Boutaghou MN, Townley IK, Zhang Q, Wang G, Cole RB, Rees BB. Analysis of tissue proteomes of the Gulf killifish, Fundulus grandis, by 2D electrophoresis and MALDI-TOF/TOF mass spectrometry. Integr Comp Biol 2012; 52:626-35. [PMID: 22537935 DOI: 10.1093/icb/ics063] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The Gulf killifish, Fundulus grandis, is a small teleost fish that inhabits marshes of the Gulf of Mexico and demonstrates high tolerance of environmental variation, making it an excellent subject for the study of physiological and molecular adaptations to environmental stress. In the present study, two-dimensional (2D) gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry were used to resolve and identify proteins from five tissues: skeletal muscle, liver, brain, heart, and gill. Of 864 protein features excised from 2D gels, 424 proteins were identified, corresponding to a 49% identification rate. For any given tissue, several protein features were identified as the same protein, resulting in a total of 254 nonredundant proteins. These nonredundant proteins were categorized into a total of 11 molecular functions, including catalytic activity, structural molecule, binding, and transport. In all tissues, catalytic activity and binding were the most highly represented molecular functions. Comparing across the tissues, proteome coverage was lowest in skeletal muscle, due to a combination of a low number of gel spots excised for analysis and a high redundancy of identifications among these spots. Nevertheless, the identification of a substantial number of proteins with high statistical confidence from other tissues suggests that F. grandis may serve as a model fish for future studies of environmental proteomics and ultimately help to elucidate proteomic responses of fish and other vertebrates to environmental stress.
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Affiliation(s)
- Naga V Abbaraju
- Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA.
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Abbaraju NV, Cai Y, Rees BB. Protein recovery and identification from the gulf killifish, Fundulus grandis: comparing snap-frozen and RNAlater® preserved tissues. Proteomics 2011; 11:4257-61. [PMID: 21898826 DOI: 10.1002/pmic.201100328] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 07/20/2011] [Accepted: 08/04/2011] [Indexed: 11/12/2022]
Abstract
Reliable proteomic analysis of biological tissues requires sampling approaches that preserve proteins as close to their in vivo state as possible. In the current study, the patterns of protein abundance in one-dimensional (1-D) gels were assessed for five tissues of the gulf killifish, Fundulus grandis, following snap-freezing tissues in liquid nitrogen or immersion of fresh tissues in RNAlater(®). In liver and heart, the protein profiles in 1-D gels were better preserved by snap-freezing, while in gill, the 1-D protein profile was better preserved by immersion in RNAlater(®). In skeletal muscle and brain, the two approaches yielded similar patterns of protein abundance. LC-MS/MS analyses and database searching resulted in the identification of 17 proteins in liver and 12 proteins in gill. Identified proteins include enzymes of energy metabolism, structural proteins, and proteins serving other biological functions. These protein identifications for a species without a sequenced genome demonstrate the utility of F. grandis as a model organism for environmental proteomic studies in vertebrates.
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Affiliation(s)
- Naga V Abbaraju
- Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA
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Lin CY, Wang V, Shui HA, Juang RH, Hour AL, Chen PS, Huang HM, Wu SY, Lee JC, Tsai TL, Chen HM. A comprehensive evaluation of imidazole-zinc reverse stain for current proteomic researches. Proteomics 2009; 9:696-709. [PMID: 19137546 DOI: 10.1002/pmic.200700470] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In this paper, we comprehensively evaluated the capability of imidazole-zinc reverse stain (ZN) in comparative proteomics. Three commonly used protein gel staining methods, including silver (SN), SYPRO Ruby (SR), and CB stain were investigated alongside for comparison purpose. A transparency scanning procedure, which may deliver more even and contrasting gel images, was found best for documenting ZN stained gels. Our results showed that ZN was more sensitive than SN, SR, and CB. It may reveal as few as 1.8 ng of proteins in a gel. Moreover, ZN was found to provide a linear dynamic range of staining for revealing proteins up to 140 ng, and show an insignificant staining preference. To analyze a ZN stained 2-D gel image that generally comprises an apparent but even background, the Melanie 4 software was found more suitable than others. Furthermore, ZN demonstrated an equivalent or better MS compatibility than the other three staining methods. Intense and comprehensive MS profiles were frequently observed for ZN stained gel spots. Approximate two-third of ZN stained gel spots were successfully identified for protein identities. Taken together, our results suggest that the prompt, cost effective and versatile ZN is well suited for current proteomic researches.
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Affiliation(s)
- Ching-Yu Lin
- Graduate Institute of Applied Science and Engineering, Catholic Fu-Jen University, Taipei, Taiwan, Republic of China
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Christiansen J, Houen G. Comparison of different staining methods for polyvinylidene difluoride membranes. Electrophoresis 1992; 13:179-83. [PMID: 1375557 DOI: 10.1002/elps.1150130137] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Several new staining methods for polyvinylidene difluoride membranes, including mercurochrome, silver and dimethylaminoazobenzene isothiocyanate staining were compared with Coomassie Brilliant Blue and gold staining. Of these, Coomassie was most versatile and completely compatible with ensuing microsequencing, immunostaining or other visualization methods, while gold and silver staining were more sensitive. Mercurochrome allows selective detection of sulfhydryl-containing proteins while dimethylaminoazobenzene isothiocyanate staining may allow quantitation of sequenceable protein.
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Affiliation(s)
- J Christiansen
- Institute of Biochemical Genetics, University of Copenhagen, Denmark
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