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Chen W, He Y, Fang C, Lu H. A rapid and convenient sample treatment method based on the dissolvable polyacrylamide gel for S-acylation proteomics. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:4590-4598. [PMID: 38920099 DOI: 10.1039/d4ay00937a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
Protein S-acylation is an important lipid modification and plays a series of biological functions. As a classic proteomic method for S-acylated proteome analysis, the acyl-biotin exchange and its derivative methods are known to be very labour-intensive and time-consuming all the time, and will result in significant sample loss. Multiple methanol-chloroform precipitations are involved in order to remove the substances that would interfere with enrichment and identification including detergents, the residual reduction and alkylation reagents. Here, we developed a rapid and convenient method for S-acylation proteomics by combining a dissolvable tube gel and the classic ABE method, a Dissolvable Gel based One-Tube sample Treatment method (DGOTT) method. The protein fixation rate, impact of the gel size on analysis performance and feasibility for analyzing complex samples were evaluated. This method enabled the alkylation and chemical substitution reactions to be conducted in a single EP tube, and convenient removal of interferents through gel washing, which could obviously simplify operations and shorten the sample treatment duration. Finally, we identified a total of 1625 potential S-acylated proteins from 800 μg of mouse brain cerebral cortex proteins. We believe that our method could offer potential for high-throughput analysis of protein S-acylation.
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Affiliation(s)
- Weiyu Chen
- Department of Chemistry and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200438, People's Republic of China.
| | - Yufei He
- Department of Chemistry and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200438, People's Republic of China.
| | - Caiyun Fang
- Department of Chemistry and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200438, People's Republic of China.
| | - Haojie Lu
- Department of Chemistry and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200438, People's Republic of China.
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, 200032, People's Republic of China
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2
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Lee OYA, Wong ANN, Ho CY, Tse KW, Chan AZ, Leung GPH, Kwan YW, Yeung MHY. Potentials of Natural Antioxidants in Reducing Inflammation and Oxidative Stress in Chronic Kidney Disease. Antioxidants (Basel) 2024; 13:751. [PMID: 38929190 PMCID: PMC11201162 DOI: 10.3390/antiox13060751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/13/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Chronic kidney disease (CKD) presents a substantial global public health challenge, with high morbidity and mortality. CKD patients often experience dyslipidaemia and poor glycaemic control, further exacerbating inflammation and oxidative stress in the kidney. If left untreated, these metabolic symptoms can progress to end-stage renal disease, necessitating long-term dialysis or kidney transplantation. Alleviating inflammation responses has become the standard approach in CKD management. Medications such as statins, metformin, and GLP-1 agonists, initially developed for treating metabolic dysregulation, demonstrate promising renal therapeutic benefits. The rising popularity of herbal remedies and supplements, perceived as natural antioxidants, has spurred investigations into their potential efficacy. Notably, lactoferrin, Boerhaavia diffusa, Amauroderma rugosum, and Ganoderma lucidum are known for their anti-inflammatory and antioxidant properties and may support kidney function preservation. However, the mechanisms underlying the effectiveness of Western medications and herbal remedies in alleviating inflammation and oxidative stress occurring in renal dysfunction are not completely known. This review aims to provide a comprehensive overview of CKD treatment strategies and renal function preservation and critically discusses the existing literature's limitations whilst offering insight into the potential antioxidant effects of these interventions. This could provide a useful guide for future clinical trials and facilitate the development of effective treatment strategies for kidney functions.
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Affiliation(s)
- On Ying Angela Lee
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China; (O.Y.A.L.)
| | - Alex Ngai Nick Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China; (O.Y.A.L.)
| | - Ching Yan Ho
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China; (O.Y.A.L.)
| | - Ka Wai Tse
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China; (O.Y.A.L.)
| | - Angela Zaneta Chan
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - George Pak-Heng Leung
- Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong SAR, China;
| | - Yiu Wa Kwan
- The School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Martin Ho Yin Yeung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China; (O.Y.A.L.)
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
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3
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Charneau S, de Oliveira LS, Zenonos Z, Hopp CS, Bastos IMD, Loew D, Lombard B, Pandolfo Silveira A, de Carvalho Nardeli Basílio Lobo G, Bao SN, Grellier P, Rayner JC. APEX2-based proximity proteomic analysis identifies candidate interactors for Plasmodium falciparum knob-associated histidine-rich protein in infected erythrocytes. Sci Rep 2024; 14:11242. [PMID: 38755230 PMCID: PMC11099048 DOI: 10.1038/s41598-024-61295-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 05/03/2024] [Indexed: 05/18/2024] Open
Abstract
The interaction of Plasmodium falciparum-infected red blood cells (iRBCs) with the vascular endothelium plays a crucial role in malaria pathology and disease. KAHRP is an exported P. falciparum protein involved in iRBC remodelling, which is essential for the formation of protrusions or "knobs" on the iRBC surface. These knobs and the proteins that are concentrated within them allow the parasites to escape the immune response and host spleen clearance by mediating cytoadherence of the iRBC to the endothelial wall, but this also slows down blood circulation, leading in some cases to severe cerebral and placental complications. In this work, we have applied genetic and biochemical tools to identify proteins that interact with P. falciparum KAHRP using enhanced ascorbate peroxidase 2 (APEX2) proximity-dependent biotinylation and label-free shotgun proteomics. A total of 30 potential KAHRP-interacting candidates were identified, based on the assigned fragmented biotinylated ions. Several identified proteins have been previously reported to be part of the Maurer's clefts and knobs, where KAHRP resides. This study may contribute to a broader understanding of P. falciparum protein trafficking and knob architecture and shows for the first time the feasibility of using APEX2-proximity labelling in iRBCs.
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Affiliation(s)
- Sébastien Charneau
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, 70910-900, Brazil.
| | - Lucas Silva de Oliveira
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, 70910-900, Brazil
- UMR 7245 MCAM Molecules of Communication and Adaptation of Microorganisms, Muséum National d'Histoire Naturelle, CNRS, 75231, Paris Cedex 05, France
| | - Zenon Zenonos
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
- Biologics Engineering, Oncology R&D, AstraZenecaGranta Park, Cambridge, UK
| | - Christine S Hopp
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
- Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Izabela M D Bastos
- Laboratory of Host Pathogen Interaction, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, 70910-900, Brazil
| | - Damarys Loew
- Institut Curie, Centre de Recherche, PSL Research University, CurieCoreTech Mass Spectrometry Proteomics, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Bérangère Lombard
- Institut Curie, Centre de Recherche, PSL Research University, CurieCoreTech Mass Spectrometry Proteomics, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Ariane Pandolfo Silveira
- Laboratory of Microscopy and Microanalysis, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, 70910-900, Brazil
| | | | - Sônia Nair Bao
- Laboratory of Microscopy and Microanalysis, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, 70910-900, Brazil
| | - Philippe Grellier
- UMR 7245 MCAM Molecules of Communication and Adaptation of Microorganisms, Muséum National d'Histoire Naturelle, CNRS, 75231, Paris Cedex 05, France
| | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK
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Mansuri MS, Bathla S, Lam TT, Nairn AC, Williams KR. Optimal conditions for carrying out trypsin digestions on complex proteomes: From bulk samples to single cells. J Proteomics 2024; 297:105109. [PMID: 38325732 PMCID: PMC10939724 DOI: 10.1016/j.jprot.2024.105109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/10/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
To identify proteins by the bottom-up mass spectrometry workflow, enzymatic digestion is essential to break down proteins into smaller peptides amenable to both chromatographic separation and mass spectrometric analysis. Trypsin is the most extensively used protease due to its high cleavage specificity and generation of peptides with desirable positively charged N- and C-terminal amino acid residues that are amenable to reverse phase HPLC separation and MS/MS analyses. However, trypsin can yield variable digestion profiles and its protein cleavage activity is interdependent on trypsin source and quality, digestion time and temperature, pH, denaturant, trypsin and substrate concentrations, composition/complexity of the sample matrix, and other factors. There is therefore a need for a more standardized, general-purpose trypsin digestion protocol. Based on a review of the literature we delineate optimal conditions for carrying out trypsin digestions of complex proteomes from bulk samples to limiting amounts of protein extracts. Furthermore, we highlight recent developments and technological advances used in digestion protocols to quantify complex proteomes from single cells. SIGNIFICANCE: Currently, bottom-up MS-based proteomics is the method of choice for global proteome analysis. Since trypsin is the most utilized protease in bottom-up MS proteomics, delineating optimal conditions for carrying out trypsin digestions of complex proteomes in samples ranging from tissues to single cells should positively impact a broad range of biomedical research.
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Affiliation(s)
- M Shahid Mansuri
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA.
| | - Shveta Bathla
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Department of Psychiatry, Yale School of Medicine, New Haven, CT 06511, USA
| | - TuKiet T Lam
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA; Keck MS & Proteomics Resource, Yale School of Medicine, New Haven, CT 06511, USA
| | - Angus C Nairn
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Department of Psychiatry, Yale School of Medicine, New Haven, CT 06511, USA
| | - Kenneth R Williams
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA; Keck MS & Proteomics Resource, Yale School of Medicine, New Haven, CT 06511, USA.
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Chou CH, Yen CH, Liu CJ, Tu HF, Lin SC, Chang KW. The upregulation of VGF enhances the progression of oral squamous carcinoma. Cancer Cell Int 2024; 24:115. [PMID: 38528565 DOI: 10.1186/s12935-024-03301-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/09/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Oral squamous cell carcinoma (OSCC) is a prevalent neoplasm worldwide, necessitating a deeper understanding of its pathogenesis. VGF nerve growth factor inducible (VGF), a neuropeptide, plays critical roles in nerve and endocrine cell regulation. METHODS In this study, the TCGA datasets were initially screened, identifying the upregulation of VGF in various malignancies. We focused on OSCC cell lines, identifying the suppressor mRNA miR-432-5p as a negative regulator of VGF. Additionally, we examined the prognostic value of VGF expression in OSCC tumors and its impact on cellular functions. RESULTS VGF expression was found to be an independent prognostic predictor in OSCC tumors. Cells expressing VGF exhibited increased oncogenicity, influencing the proliferation and migration of oral mucosal fibroblast. Transcriptome analysis revealed associations between VGF and various pathological processes, including malignancies, exosome release, fibrosis, cell cycle disruption, and tumor immune suppression. Moreover, IL23R expression, a favorable OSCC prognostic factor, was inversely correlated with VGF expression. Exogenous IL23R expression was found to suppress VGF-associated mobility phenotypes. CONCLUSIONS This study highlights the multifaceted role of VGF in OSCC pathogenesis and introduces the miR-432-5p-VGF-IL23R regulatory axis as a critical mediator. The combined expression of VGF and IL23R emerges as a potent predictor of survival in oral carcinoma cases, suggesting potential implications for future therapeutic strategies.
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Affiliation(s)
- Chung-Hsien Chou
- Institute of Oral Biology, College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chun-Han Yen
- Institute of Oral Biology, College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chung-Ji Liu
- Department of Dentistry, College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Stomatology, Taipei Mackay Memorial Hospital, Taipei, Taiwan
| | - Hsi-Feng Tu
- Institute of Oral Biology, College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Dentistry, College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Shu-Chun Lin
- Institute of Oral Biology, College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan.
- Department of Dentistry, College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan.
- Department of Stomatology, Taipei Veterans General Hospital, Taipei, Taiwan.
| | - Kuo-Wei Chang
- Institute of Oral Biology, College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan.
- Department of Dentistry, College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan.
- Department of Stomatology, Taipei Veterans General Hospital, Taipei, Taiwan.
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6
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Rani A, Pandey DM, Pandey JP. Identification of cocoonase and cocoonase like protein using polyclonal antibody of Antheraea mylitta cocoonase. Biotechnol Lett 2024; 46:47-54. [PMID: 38109018 DOI: 10.1007/s10529-023-03447-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 10/03/2023] [Accepted: 11/04/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND Cocoonase is a proteolytic enzyme released by silk moths during pupal adult emergence. Without damaging the silk fibroin, this enzyme dissolves the shell of the tasar cocoon by exclusively targeting the protein sericin. Prior to this study, there was no available antibody against Antheraea mylitta cocoonase to identify or screen out similar variants or cocoonase like protein. RESULTS In the present study, naturally secreted A. mylitta cocoonase was purified and used to immunize New Zealand white rabbits. The developed polyclonal antibody of cocoonase was purified and its specific interaction with cocoonase was determined using Indirect ELISA. The confirmation of its specificity and immuno-reactivity was evaluated by western blot using native cocoonase of tasar silkworm A. mylitta. The efficacy and specificity of the polyclonal antibody were further verified and confirmed by western blot which was performed to detect ten different ecotypes of A. mylitta cocoonase. CONCLUSION The developed antibody successfully detected the cocoonase of different ecotypes. Thus, in future this antibody can serve as one of the molecular detection method for cocoonase and cocoonase-like proteins.
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Affiliation(s)
- Aruna Rani
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
- Biotechnology Division, Central Tasar Research and Training Institute (Central Silk Board, Ministry of Textiles), Piska Nagri, Ranchi, Jharkhand, 835303, India
| | - Dev Mani Pandey
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India.
| | - Jay Prakash Pandey
- Biotechnology Division, Central Tasar Research and Training Institute (Central Silk Board, Ministry of Textiles), Piska Nagri, Ranchi, Jharkhand, 835303, India.
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Heng B, Pires AS, Chow S, Krishnamurthy S, Bonnell B, Bustamante S, Guillemin GJ. Stability Studies of Kynurenine Pathway Metabolites in Blood Components Define Optimal Blood Processing Conditions. Int J Tryptophan Res 2023; 16:11786469231213521. [PMID: 38106464 PMCID: PMC10725091 DOI: 10.1177/11786469231213521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/25/2023] [Indexed: 12/19/2023] Open
Abstract
The kynurenine pathway (KP) is the main pathway of tryptophan (TRP) metabolism that generates energy for multiple cellular processes. The activity of this pathway has been shown to be dysregulated in multiple human diseases. The resultant modulation of metabolites has been suggested to comprise biomarkers to track disease progression or could identify new therapeutic targets. While metabolite changes can be measured readily in blood, there is limited knowledge on the effect of blood matrices and sample processing time may have on the stability of KP metabolites. Understanding the stability of KP metabolites in blood is integral to obtaining accurate KP data to correlate with clinical pathology. Hence, the aim of this study was to assess the concentration of KP metabolites in matched whole blood, plasma and serum. The impact of pre-analytical sample processing time in the various blood matrices was also analysed. Serum and plasma had the higher concentration of KP metabolites compared to whole blood. Furthermore, concentrations of KP metabolites declined when the collected blood was processed after 24 hours storage at 4°C. Our study shows that that type of blood matrix and the time to processing have an impact on the stability of the KP metabolites. Serum or plasma are the preferred choice of matrix and the isolation of these matrices from whole blood is best performed immediately after collection for optimal analytical KP data.
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Affiliation(s)
- Benjamin Heng
- Macquarie Medical School, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ananda Staats Pires
- Macquarie Medical School, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Sharron Chow
- Macquarie Medical School, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Shivani Krishnamurthy
- Macquarie Medical School, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Brooke Bonnell
- Macquarie Medical School, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Sonia Bustamante
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, Australia
| | - Gilles J Guillemin
- Macquarie Medical School, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
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Cirillo F, Talia M, Santolla MF, Pellegrino M, Scordamaglia D, Spinelli A, De Rosis S, Giordano F, Muglia L, Zicarelli A, Di Dio M, Rigiracciolo DC, Miglietta AM, Filippelli G, De Francesco EM, Belfiore A, Lappano R, Maggiolini M. GPER deletion triggers inhibitory effects in triple negative breast cancer (TNBC) cells through the JNK/c-Jun/p53/Noxa transduction pathway. Cell Death Discov 2023; 9:353. [PMID: 37749101 PMCID: PMC10520078 DOI: 10.1038/s41420-023-01654-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/28/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023] Open
Abstract
The G protein-coupled estrogen receptor (GPER) mediates estrogen action in different pathophysiological conditions, including cancer. GPER expression and signaling have been found to join in the progression of triple-negative breast cancer (TNBC), even though controversial data have been reported. In present study, we aimed at providing new mechanistic and biological discoveries knocking out (KO) GPER expression by CRISPR/Cas9 technology in MDA-MB-231 TNBC cells. GPER KO whole transcriptome respect to wild type (WT) MDA-MB-231 cells was determined through total RNA sequencing (RNA-Seq) and gene ontology (GO) enrichment analysis. We ascertained that anti-proliferative and pro-apoptotic gene signatures characterize GPER KO MDA-MB-231 cells. Thereafter, we determined that these cells exhibit a reduced proliferative, clonogenic and self-renewal potential along with an increased mitochondria-dependent apoptosis phenotype. In addition, we recognized that decreased cAMP levels trigger the JNK/c-Jun/p53/Noxa axis, which in turn orchestrates the pro-apoptotic effects observed in GPER KO cells. In accordance with these data, survival analyses in TNBC patients of the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) dataset indicated that high Noxa expression correlates with improved outcomes in TNBC patients. Furthermore, we demonstrated that GPER KO in TNBC cells impairs the expression and secretion of the well-acknowledged GPER target gene named CTGF, thus resulting in the inhibition of migratory effects in cancer-associated fibroblasts (CAFs). Overall, the present study provides novel mechanistic and biological insights on GPER KO in TNBC cells suggesting that GPER may be considered as a valuable target in comprehensive therapeutic approaches halting TNBC progression.
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Affiliation(s)
- Francesca Cirillo
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036, Rende, Italy
| | - Marianna Talia
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036, Rende, Italy
| | - Maria Francesca Santolla
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036, Rende, Italy
| | - Michele Pellegrino
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036, Rende, Italy
| | - Domenica Scordamaglia
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036, Rende, Italy
| | - Asia Spinelli
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036, Rende, Italy
| | - Salvatore De Rosis
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036, Rende, Italy
| | - Francesca Giordano
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036, Rende, Italy
| | - Lucia Muglia
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036, Rende, Italy
| | - Azzurra Zicarelli
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036, Rende, Italy
| | - Marika Di Dio
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036, Rende, Italy
| | - Damiano Cosimo Rigiracciolo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milano, Italy
| | - Anna Maria Miglietta
- Breast and General Surgery Unit, Regional Hospital Cosenza, 87100, Cosenza, Italy
| | | | - Ernestina Marianna De Francesco
- Endocrinology, Department of Clinical and Experimental Medicine, University of Catania, Garibaldi-Nesima Hospital, 95122, Catania, Italy
| | - Antonino Belfiore
- Endocrinology, Department of Clinical and Experimental Medicine, University of Catania, Garibaldi-Nesima Hospital, 95122, Catania, Italy
| | - Rosamaria Lappano
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036, Rende, Italy.
| | - Marcello Maggiolini
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036, Rende, Italy.
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9
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Liu Z, Wong ILK, Sang J, Liu F, Yan CSW, Kan JWY, Chan TH, Chow LMC. Identification of Binding Sites in the Nucleotide-Binding Domain of P-Glycoprotein for a Potent and Nontoxic Modulator, the Amine-Containing Monomeric Flavonoid FM04. J Med Chem 2023; 66:6160-6183. [PMID: 37098275 DOI: 10.1021/acs.jmedchem.2c02005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
We have previously discovered an amine-containing flavonoid monomer FM04 as a potent P-glycoprotein (P-gp) inhibitor (EC50 = 83 nM). Here, a series of photoactive FM04 analogues were synthesized and used together with liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify the FM04-binding sites on P-gp. Point mutations around the photo-crosslinked sites were made for verification. Together with the results from mutational studies, molecular docking, and molecular dynamics simulations, it was found that FM04 can interact with Q1193 and I1115 in the nucleotide-binding domain 2 (NBD2) of human P-gp. It was proposed that FM04 can inhibit P-gp in 2 novel mechanisms. FM04 can either bind to (1) Q1193, followed by interacting with the functionally critical residues H1195 and T1226 or (2) I1115 (a functionally critical residue itself), disrupting the R262-Q1081-Q1118 interaction pocket and uncoupling ICL2-NBD2 interaction and thereby inhibiting P-gp. Q1118 would subsequently be pushed to the ATP-binding site and stimulate ATPase.
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Affiliation(s)
- Zhen Liu
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Iris L K Wong
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Jingcheng Sang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Fufeng Liu
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong SAR, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Clare S W Yan
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Jason W Y Kan
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Tak Hang Chan
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong SAR, China
- Department of Chemistry, McGill University, Montreal, Quebec H3A 2K6, Canada
| | - Larry M C Chow
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong SAR, China
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10
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Miller RM, Perkins GL, Bush D, Tartiere A, DeGraan‐Weber N. Glycopeptide characterization of Sf9-derived SARS-CoV-2 spike protein recombinant vaccine candidates expedited by the use of glycopeptide libraries. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9452. [PMID: 36478308 PMCID: PMC9877958 DOI: 10.1002/rcm.9452] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
RATIONALE We report the N-glycosylation pattern of Sf9 insect cell-derived recombinant spike proteins being developed as candidate vaccine antigens for SARS-CoV-2 (COVID-19) (Sanofi). The method has been optimised to produce peptides with single, isolated glycosylation sites using multiple protease digests. The development and use of glycopeptide libraries from previous developmental phases allowed for faster analysis than processing datasets from individual batches from first principles. METHODS Purified spike proteins were reduced, alkylated, and digested with proteolytic enzymes. Three different protease digests were utilised to generate peptides with isolated glycosylation sites. The glycopeptides were then analysed using a Waters Q-TOF while using a data-dependent acquisition mass spectrometry experiment. Glycopeptide mapping data processing and glycan classification were performed using Genedata Expressionist via a specialised workflow that used libraries of previously detected glycopeptides to greatly reduce processing time. RESULTS Two different spike proteins from six manufacturers were analysed. There was a strong similarity at each site across batches and manufacturers. The majority of the glycans present were of the truncated class, although at sites N61, N234, and N717/714 high mannose structures were dominant and at N1173/1170 aglycosylation was dominant for both variant proteins. A comparison was performed on a commercially available spike protein and our results were found to be similar to those of earlier reports. CONCLUSIONS Our data clearly show that the overall glycosylation pattern of both spike protein variants was highly similar from batch to batch, and between materials produced at different manufacturing facilities. The use of our glycopeptide libraries greatly expedited the generation of site-specific glycan occupancy data for a large glycoprotein. We compared our method with previously obtained data from a commercially available insect cell-derived spike protein and the results were comparable to published findings.
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11
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3-Methoxytyrosine as an indicator of dopaminergic manipulation in equine plasma. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1220:123652. [PMID: 36933516 DOI: 10.1016/j.jchromb.2023.123652] [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: 11/09/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/09/2023]
Abstract
The use of catechol-O-methyltransferase inhibitors may mask doping agents, primarily levodopa, administered to racehorses and prolong the stimulating effects of dopaminergic compounds such as dopamine. It is known that 3-methoxytyramine is a metabolite of dopamine and 3-methoxytyrosine is a metabolite of levodopa thus these compounds are proposed to be potential biomarkers of interest. Previous research established a urinary threshold of 4,000 ng/mL for 3-methoxytyramine to monitor misuse of dopaminergic agents. However, there is no equivalent biomarker in plasma. To address this deficiency a rapid protein precipitation method was developed and validated to isolate target compounds from 100 µL equine plasma. A liquid chromatography-high resolution accurate mass (LC-HRAM) method using an IMTAKT Intrada amino acid column provided quantitative analysis of 3-methoxytyrosine (3-MTyr) with lower limit of quantification of 5 ng/mL. Reference population profiling (n = 1129) investigated the expected basal concentrations for raceday samples from equine athletes and showed a right-skewed distribution (skewness = 2.39, kurtosis = 10.65) which resulted from large variation (RSD = 71%) within the data. Logarithmic transformation of the data provided a normal distribution (skewness = 0.26, kurtosis = 3.23) resulting in the proposal of a conservative threshold for plasma 3-MTyr of 1,000 ng/mL at a 99.995% confidence level. A 12-horse administration study of Stalevo® (800 mg L-DOPA, 200 mg carbidopa, 1600 mg entacapone) revealed elevated 3-MTyr concentrations for 24-hours post-administration.
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12
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Crocin Attenuates NLRP3 Inflammasome Activation by Inhibiting Mitochondrial Reactive Oxygen Species and Ameliorates Monosodium Urate-Induced Mouse Peritonitis. Curr Issues Mol Biol 2023; 45:2090-2104. [PMID: 36975504 PMCID: PMC10047758 DOI: 10.3390/cimb45030134] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
Crocin is a hydrophilic carotenoid pigment found in the stigma of Crocus sativus or the fruit of Gardenia jasminoides. In this study, we investigated the effects of Crocin on the activation of the nucleotide-binding oligomerization domain, leucine-rich repeat, and pyrin domain containing 3 (NLRP3) inflammasome in J774A.1 murine macrophage cells and monosodium urate (MSU)-induced peritonitis. Crocin significantly inhibited Nigericin-, adenosine triphosphate (ATP)-, MSU-induced interleukin (IL)-1β secretion, and caspase-1 cleavage without affecting pro-IL-1β and pro-caspase-1. Crocin also suppressed gasdermin-D cleavage and lactate dehydrogenase release and enhanced cell viability, indicating that Crocin reduces pyroptosis. Similar effects were observed in primary mouse macrophages. However, Crocin did not affect poly(dA:dT)-induced absent in melanoma 2 (AIM2) and muramyl dipeptide-induced NLRP1 inflammasomes. Crocin decreased Nigericin-induced oligimerization and the speck formation of apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC). Crocin also dramatically alleviated the ATP-induced production of mitochondrial reactive oxygen species (mtROS). Finally, Crocin ameliorated the MSU-induced production of IL-1β and IL-18 and the recruitment of neutrophils during peritoneal inflammation. These results suggest that Crocin suppresses NLRP3 inflammasome activation by blocking mtROS production and ameliorates MSU-induced mouse peritonitis. Thus, Crocin may have therapeutic potential in various NLRP3 inflammasome-related inflammatory diseases.
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13
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Shen S, Wang X, Zhu X, Rasam S, Ma M, Huo S, Qian S, Zhang M, Qu M, Hu C, Jin L, Tian Y, Sethi S, Poulsen D, Wang J, Tu C, Qu J. High-quality and robust protein quantification in large clinical/pharmaceutical cohorts with IonStar proteomics investigation. Nat Protoc 2023; 18:700-731. [PMID: 36494494 PMCID: PMC10673696 DOI: 10.1038/s41596-022-00780-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 09/22/2022] [Indexed: 12/14/2022]
Abstract
Robust, reliable quantification of large sample cohorts is often essential for meaningful clinical or pharmaceutical proteomics investigations, but it is technically challenging. When analyzing very large numbers of samples, isotope labeling approaches may suffer from substantial batch effects, and even with label-free methods, it becomes evident that low-abundance proteins are not reliably measured owing to unsufficient reproducibility for quantification. The MS1-based quantitative proteomics pipeline IonStar was designed to address these challenges. IonStar is a label-free approach that takes advantage of the high sensitivity/selectivity attainable by ultrahigh-resolution (UHR)-MS1 acquisition (e.g., 120-240k full width at half maximum at m/z = 200) which is now widely available on ultrahigh-field Orbitrap instruments. By selectively and accurately procuring quantitative features of peptides within precisely defined, very narrow m/z windows corresponding to the UHR-MS1 resolution, the method minimizes co-eluted interferences and substantially enhances signal-to-noise ratio of low-abundance species by decreasing noise level. This feature results in high sensitivity, selectivity, accuracy and precision for quantification of low-abundance proteins, as well as fewer missing data and fewer false positives. This protocol also emphasizes the importance of well-controlled, robust experimental procedures to achieve high-quality quantification across a large cohort. It includes a surfactant cocktail-aided sample preparation procedure that achieves high/reproducible protein/peptide recoveries among many samples, and a trapping nano-liquid chromatography-mass spectrometry strategy for sensitive and reproducible acquisition of UHR-MS1 peptide signal robustly across a large cohort. Data processing and quality evaluation are illustrated using an example dataset ( http://proteomecentral.proteomexchange.org ), and example results from pharmaceutical project and one clinical project (patients with acute respiratory distress syndrome) are shown. The complete IonStar pipeline takes ~1-2 weeks for a sample cohort containing ~50-100 samples.
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Affiliation(s)
- Shichen Shen
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Xue Wang
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
- AbbVie Bioresearch Center, Worcester, MA, USA
| | - Xiaoyu Zhu
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Sailee Rasam
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Min Ma
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Shihan Huo
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Shuo Qian
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Ming Zhang
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Miao Qu
- Department of Neurology, Xuanwu Hospital, Beijing, China
| | - Chenqi Hu
- AbbVie Bioresearch Center, Worcester, MA, USA
| | - Liang Jin
- AbbVie Bioresearch Center, Worcester, MA, USA
| | - Yu Tian
- AbbVie Bioresearch Center, Worcester, MA, USA
| | - Sanjay Sethi
- Department of Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - David Poulsen
- Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Chengjian Tu
- BioProduction Group, Thermo Fisher Scientific, Buffalo, NY, USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA.
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14
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Shintani T, Suzuki R, Takeuchi Y, Shirasawa T, Noda M. Deletion or inhibition of PTPRO prevents ectopic fat accumulation and induces healthy obesity with markedly reduced systemic inflammation. Life Sci 2023; 313:121292. [PMID: 36535401 DOI: 10.1016/j.lfs.2022.121292] [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: 11/02/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
AIMS Chronic inflammation plays crucial roles in obesity-induced metabolic diseases. Protein tyrosine phosphatase receptor type O (PTPRO) is a member of the R3 subfamily of receptor-like protein tyrosine phosphatases. We previously suggested a role for PTPRO in the inactivation of the insulin receptor. The present study aimed to elucidate the involvement of PTPRO in the control of glucose and lipid metabolism as well as in obesity-induced systemic inflammation. MATERIALS AND METHODS Lipid accumulation in adipose tissue and the liver, the expression of inflammatory cytokines, and insulin resistance associated with systemic inflammation were investigated in hyper-obese Ptpro-KO mice by feeding a high-fat/high-sucrose diet (HFHSD). The effects of the administration of AKB9778, a specific inhibitor of PTPRO, to ob/ob mice and cultured 3T3-L1 preadipocyte cells were also examined. KEY FINDINGS Ptpro was highly expressed in visceral white adipose tissue and macrophages. Ptpro-KO mice fed HFHSD were hyper-obese, but did not have ectopic fat accumulation in the liver, dysfunctional lipid and glucose homeostasis, systemic inflammation, or insulin resistance. The administration of AKB9778 reproduced "the healthy obese phenotypes" of Ptpro-KO mice in highly obese ob/ob mice. Furthermore, the inhibition of PTPRO promoted the growth of lipid droplets in adipocytes through an increase in the phosphorylation of Tyr(117) in vimentin. SIGNIFICANCE Healthy systemic conditions with the attenuation of inflammation in hyper-obese Ptpro-KO mice were associated with the expansion of adipose tissue and low activation of NF-κb. Therefore, PTPRO may be a promising target to ameliorate hepatic steatosis and metabolic dysfunction.
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Affiliation(s)
- Takafumi Shintani
- Homeostatic Mechanism Research Unit, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan; Division of Molecular Neurobiology, National Institute for Basic Biology, Okazaki, Aichi 444-8787, Japan
| | - Ryoko Suzuki
- Division of Molecular Neurobiology, National Institute for Basic Biology, Okazaki, Aichi 444-8787, Japan
| | - Yasushi Takeuchi
- Division of Molecular Neurobiology, National Institute for Basic Biology, Okazaki, Aichi 444-8787, Japan
| | | | - Masaharu Noda
- Homeostatic Mechanism Research Unit, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan; Division of Molecular Neurobiology, National Institute for Basic Biology, Okazaki, Aichi 444-8787, Japan.
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15
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Wilder SM, Barnes CL. Comparing the accuracy of protein measures for arthropods. JOURNAL OF INSECT PHYSIOLOGY 2023; 144:104470. [PMID: 36525989 DOI: 10.1016/j.jinsphys.2022.104470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 11/30/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Data on the protein content of arthropods can be useful for addressing a variety of ecological, behavioral, and physiological hypotheses. Yet, the most accurate method for measuring protein content (i.e., amino acid analysis) is expensive and the accuracy of less expensive measures of protein is unclear. We analyzed a diversity of arthropods to test for relationships between digestible protein content as measured by amino acid analysis and several common protein measures: crude protein, Bradford assay, BCA assay, and Lowry assay. In the full dataset, the closest relationship to the amino acid data was found for the Lowry assay and the average of the Bradford and Lowry assays. However, one species, Blattella germanica, appeared to be an outlier in some analyses. When the data were analyzed without B. germanica, the closest relationships to the amino acid data were found for the Lowry assay. Our results suggest that not all protein measures are equal in their ability to estimate amino acid content. Some arthropod species can also contain chemicals that interfere with the accuracy of protein assays. Given that it is unclear how often interfering compounds are found in invertebrates, it may be best to conduct multiple assays when analyzing the protein content of arthropods, especially the Bradford and Lowry assays.
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Affiliation(s)
- Shawn M Wilder
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA.
| | - Cody L Barnes
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA
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16
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Sharma A, Meer M, Dapkunas A, Ihermann-Hella A, Kuure S, Vainio SJ, Iber D, Naillat F. FGF8 induces chemokinesis and regulates condensation of mouse nephron progenitor cells. Development 2022; 149:277149. [DOI: 10.1242/dev.201012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022]
Abstract
ABSTRACT
Kidneys develop via iterative branching of the ureteric epithelial tree and subsequent nephrogenesis at the branch points. Nephrons form in the cap mesenchyme as the metanephric mesenchyme (MM) condenses around the epithelial ureteric buds (UBs). Previous work has demonstrated that FGF8 is important for the survival of nephron progenitor cells (NPCs), and early deletion of Fgf8 leads to the cessation of nephron formation, which results in post-natal lethality. We now reveal a previously unreported function of FGF8. By combining transgenic mouse models, quantitative imaging assays and data-driven computational modelling, we show that FGF8 has a strong chemokinetic effect and that this chemokinetic effect is important for the condensation of NPCs to the UB. The computational model shows that the motility must be lower close to the UB to achieve NPC attachment. We conclude that the FGF8 signalling pathway is crucial for the coordination of NPC condensation at the UB. Chemokinetic effects have also been described for other FGFs and may be generally important for the formation of mesenchymal condensates.
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Affiliation(s)
- Abhishek Sharma
- University of Oulu 1 Faculty of Biochemistry and Molecular Medicine , , Oulu 90220, Finland
- Biocenter Oulu 2 , Oulu 90220, Finland
| | - Marco Meer
- ETH Zürich 3 Department of Biosystems, Science and Engineering , , Zürich 04058, Switzerland
- Swiss Institute of Bioinformatics 4 , Lausanne 1015 , Switzerland
| | - Arvydas Dapkunas
- University of Helsinki 5 HiLIFE and Research Programs Unit, Faculty of Medicine , , Helsinki 00014, Finland
| | - Anneliis Ihermann-Hella
- University of Helsinki 5 HiLIFE and Research Programs Unit, Faculty of Medicine , , Helsinki 00014, Finland
| | - Satu Kuure
- University of Helsinki 5 HiLIFE and Research Programs Unit, Faculty of Medicine , , Helsinki 00014, Finland
- LAC/HiLIFE, and Medicum, University of Helsinki 6 GM-Unit , , Helsinki 00014, Finland
| | - Seppo J. Vainio
- University of Oulu 1 Faculty of Biochemistry and Molecular Medicine , , Oulu 90220, Finland
- Biocenter Oulu 2 , Oulu 90220, Finland
- Infotech Oulu 7 , Oulu 90200, Finland
- Borealis Biobank 8 , Oulu 90200, Finland
- Kvantum Institute, University of Oulu 9 , Oulu 90200, Finland
| | - Dagmar Iber
- ETH Zürich 3 Department of Biosystems, Science and Engineering , , Zürich 04058, Switzerland
- Swiss Institute of Bioinformatics 4 , Lausanne 1015 , Switzerland
| | - Florence Naillat
- University of Oulu 1 Faculty of Biochemistry and Molecular Medicine , , Oulu 90220, Finland
- Biocenter Oulu 2 , Oulu 90220, Finland
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17
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Varnavides G, Madern M, Anrather D, Hartl N, Reiter W, Hartl M. In Search of a Universal Method: A Comparative Survey of Bottom-Up Proteomics Sample Preparation Methods. J Proteome Res 2022; 21:2397-2411. [PMID: 36006919 PMCID: PMC9552232 DOI: 10.1021/acs.jproteome.2c00265] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Robust, efficient, and reproducible protein extraction
and sample
processing is a key step for bottom-up proteomics analyses. While
many sample preparation protocols for mass spectrometry have been
described, selecting an appropriate method remains challenging since
some protein classes may require specialized solubilization, precipitation,
and digestion procedures. Here, we present a comprehensive comparison
of the 16 most widely used sample preparation methods, covering in-solution
digests, device-based methods, and commercially available kits. We
find a remarkably good performance of the majority of the protocols
with high reproducibility, little method dependency, and low levels
of artifact formation. However, we revealed method-dependent differences
in the recovery of specific protein features, which we summarized
in a descriptive guide matrix. Our work thereby provides a solid basis
for the selection of MS sample preparation strategies for a given
proteomics project.
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Affiliation(s)
- Gina Varnavides
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Moritz Madern
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria.,Center for Molecular Biology, Department of Biochemistry and Cell Biology, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Dorothea Anrather
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Natascha Hartl
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria.,Center for Molecular Biology, Department of Biochemistry and Cell Biology, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Wolfgang Reiter
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria.,Center for Molecular Biology, Department of Biochemistry and Cell Biology, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Markus Hartl
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria.,Center for Molecular Biology, Department of Biochemistry and Cell Biology, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
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18
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Cör Andrejč D, Knez Ž, Knez Marevci M. Antioxidant, antibacterial, antitumor, antifungal, antiviral, anti-inflammatory, and nevro-protective activity of Ganoderma lucidum: An overview. Front Pharmacol 2022; 13:934982. [PMID: 35935849 PMCID: PMC9353308 DOI: 10.3389/fphar.2022.934982] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/27/2022] [Indexed: 01/20/2023] Open
Abstract
Ganoderma lucidum is a very medicinal mushroom that has been utilized in Oriental medicine for many years. It has a wide range of pharmacological and therapeutic properties, and has been used for many years as a health promoter. It contains various biologically active compounds that improve the immune system and have antioxidant, antitumor, anti-inflammatory, antifungal, and antimicrobial properties. Active compounds include triterpenoids and polysaccharides, as well as proteins, lipids, phenolics, sterols, etc. In the following review, we summarize briefly their biological activities, such as antioxidant, anti-bacterial, anti-fungal, antitumor, anti-viral, and anti-inflammatory activity. Although Ganoderma has a number of medicinal effects that have been confirmed by the in vitro and in vivo studies summarised in this review, there are some limitations. Clinical trials face mainly a lack of pure constituents. Accurate identification of the compounds obtained is also problematic. In addition, most of the included studies were small, and there were concerns about the methodological quality of each study. Studies have shown that Ganoderma has valuable potential for the prevention and treatment of cancer. In any case, G. lucidum cannot be used as first-line therapy for cancer.
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Affiliation(s)
| | - Željko Knez
- Faculty of Chemistry and Chemical Engineering, Maribor, Slovenia.,Laboratory Faculty of Medicine, Maribor, Slovenia
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The AGEs/RAGE Transduction Signaling Prompts IL-8/CXCR1/2-Mediated Interaction between Cancer-Associated Fibroblasts (CAFs) and Breast Cancer Cells. Cells 2022; 11:cells11152402. [PMID: 35954247 PMCID: PMC9368521 DOI: 10.3390/cells11152402] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/29/2022] [Accepted: 08/02/2022] [Indexed: 01/27/2023] Open
Abstract
Advanced glycation end products (AGEs) and the cognate receptor, named RAGE, are involved in metabolic disorders characterized by hyperglycemia, type 2 diabetes mellitus (T2DM) and obesity. Moreover, the AGEs/RAGE transduction pathway prompts a dysfunctional interaction between breast cancer cells and tumor stroma toward the acquisition of malignant features. However, the action of the AGEs/RAGE axis in the main players of the tumor microenvironment, named breast cancer-associated fibroblasts (CAFs), remains to be fully explored. In the present study, by chemokine array, we first assessed that interleukin-8 (IL-8) is the most up-regulated pro-inflammatory chemokine upon AGEs/RAGE activation in primary CAFs, obtained from breast tumors. Thereafter, we ascertained that the AGEs/RAGE signaling promotes a network cascade in CAFs, leading to the c-Fos-dependent regulation of IL-8. Next, using a conditioned medium from AGEs-exposed CAFs, we determined that IL-8/CXCR1/2 paracrine activation induces the acquisition of migratory and invasive features in MDA-MB-231 breast cancer cells. Altogether, our data provide new insights on the involvement of IL-8 in the AGEs/RAGE transduction pathway among the intricate connections linking breast cancer cells to the surrounding stroma. Hence, our findings may pave the way for further investigations to define the role of IL-8 as useful target for the better management of breast cancer patients exhibiting metabolic disorders.
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Jayawardena N, McCarthy C, Wang I, Waqqar S, Burga LN, Strauss M, Bostina M. Characterisation of a Seneca Valley virus thermostable mutant. Virology 2022; 575:74-82. [DOI: 10.1016/j.virol.2022.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/30/2022]
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21
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Ishimoto T, Okada T, Fujisaka S, Yagi K, Tobe K, Toyooka N, Mori H. A New Method for Albuminuria Measurement Using a Specific Reaction between Albumin and the Luciferin of the Firefly Squid Watasenia scintillans. Int J Mol Sci 2022; 23:ijms23158342. [PMID: 35955470 PMCID: PMC9368953 DOI: 10.3390/ijms23158342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 02/01/2023] Open
Abstract
This study demonstrates that the luciferin of the firefly squid Watasenia scintillans, which generally reacts with Watasenia luciferase, reacted with human albumin to emit light in proportion to the albumin concentration. The luminescence showed a peak wavelength at 540 nm and was eliminated by heat or protease treatment. We used urine samples collected from patients with diabetes to quantify urinary albumin concentration, which is essential for the early diagnosis of diabetic nephropathy. Consequently, we were able to measure urinary albumin concentrations by precipitating urinary proteins with acetone before the reaction with luciferin. A correlation was found with the result of the immunoturbidimetric method; however, the Watasenia luciferin method tended to produce lower albumin concentrations. This may be because the Watasenia luciferin reacts with only intact albumin. Therefore, the quantification method using Watasenia luciferin is a new principle of urinary albumin measurement that differs from already established methods such as immunoturbidimetry and high-performance liquid chromatography.
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Affiliation(s)
- Tetsuya Ishimoto
- Department of Molecular Neuroscience, Faculty of Medicine, University of Toyama, 2630 Sugitani, Toyama City, Toyama 930-0194, Japan;
- Research Center for Idling Brain Science, University of Toyama, 2630 Sugitani, Toyama City, Toyama 930-0194, Japan
- Correspondence:
| | - Takuya Okada
- Faculty of Engineering, University of Toyama, 3190 Gofuku, Toyama City, Toyama 930-8555, Japan; (T.O.); (N.T.)
| | - Shiho Fujisaka
- First Department of Internal Medicine, Faculty of Medicine, University of Toyama, 2630 Sugitani, Toyama City, Toyama 930-0194, Japan; (S.F.); (K.Y.); (K.T.)
| | - Kunimasa Yagi
- First Department of Internal Medicine, Faculty of Medicine, University of Toyama, 2630 Sugitani, Toyama City, Toyama 930-0194, Japan; (S.F.); (K.Y.); (K.T.)
- Department of Internal Medicine, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa 920-0293, Japan
| | - Kazuyuki Tobe
- First Department of Internal Medicine, Faculty of Medicine, University of Toyama, 2630 Sugitani, Toyama City, Toyama 930-0194, Japan; (S.F.); (K.Y.); (K.T.)
| | - Naoki Toyooka
- Faculty of Engineering, University of Toyama, 3190 Gofuku, Toyama City, Toyama 930-8555, Japan; (T.O.); (N.T.)
- Research Center for Pre-Disease Science, University of Toyama, 2630 Sugitani, Toyama City, Toyama 930-0194, Japan
| | - Hisashi Mori
- Department of Molecular Neuroscience, Faculty of Medicine, University of Toyama, 2630 Sugitani, Toyama City, Toyama 930-0194, Japan;
- Research Center for Idling Brain Science, University of Toyama, 2630 Sugitani, Toyama City, Toyama 930-0194, Japan
- Research Center for Pre-Disease Science, University of Toyama, 2630 Sugitani, Toyama City, Toyama 930-0194, Japan
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22
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Johnston HE, Yadav K, Kirkpatrick JM, Biggs GS, Oxley D, Kramer HB, Samant RS. Solvent Precipitation SP3 (SP4) Enhances Recovery for Proteomics Sample Preparation without Magnetic Beads. Anal Chem 2022; 94:10320-10328. [PMID: 35848328 PMCID: PMC9330274 DOI: 10.1021/acs.analchem.1c04200] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Complete, reproducible extraction of protein material
is essential
for comprehensive and unbiased proteome analyses. A current gold standard
is single-pot, solid-phase-enhanced sample preparation (SP3), in which
organic solvent and magnetic beads are used to denature and capture
protein aggregates, with subsequent washes removing contaminants.
However, SP3 is dependent on effective protein immobilization onto
beads, risks losses during wash steps, and exhibits losses and greater
costs at higher protein inputs. Here, we propose solvent precipitation
SP3 (SP4) as an alternative to SP3 protein cleanup, capturing acetonitrile-induced
protein aggregates by brief centrifugation rather than magnetism—with
optional low-cost inert glass beads to simplify handling. SP4 recovered
equivalent or greater protein yields for 1–5000 μg preparations
and improved reproducibility (median protein R2 0.99 (SP4) vs 0.97 (SP3)). Deep proteome
profiling revealed that SP4 yielded a greater recovery of low-solubility
and transmembrane proteins than SP3, benefits to aggregating protein
using 80 vs 50% organic solvent, and equivalent recovery by SP4 and S-Trap.
SP4 was verified in three other labs across eight sample types and
five lysis buffers—all confirming equivalent or improved proteome
characterization vs SP3. With near-identical recovery,
this work further illustrates protein precipitation as the primary
mechanism of SP3 protein cleanup and identifies that magnetic capture
risks losses, especially at higher protein concentrations and among
more hydrophobic proteins. SP4 offers a minimalistic approach to protein
cleanup that provides cost-effective input scalability, the option
to omit beads entirely, and suggests important considerations for
SP3 applications—all while retaining the speed and compatibility
of SP3.
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Affiliation(s)
- Harvey E Johnston
- Signalling Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Kranthikumar Yadav
- Mass Spectrometry Facility, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | | | - George S Biggs
- Proteomics STP, The Francis Crick Institute, London NW1 1AT, United Kingdom.,GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, Hertfordshire, United Kingdom
| | - David Oxley
- Mass Spectrometry Facility, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Holger B Kramer
- Medical Research Council London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital, London W12 0NN, United Kingdom
| | - Rahul S Samant
- Signalling Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
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23
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Scordamaglia D, Cirillo F, Talia M, Santolla MF, Rigiracciolo DC, Muglia L, Zicarelli A, De Rosis S, Giordano F, Miglietta AM, De Francesco EM, Vella V, Belfiore A, Lappano R, Maggiolini M. Metformin counteracts stimulatory effects induced by insulin in primary breast cancer cells. J Transl Med 2022; 20:263. [PMID: 35672854 PMCID: PMC9172136 DOI: 10.1186/s12967-022-03463-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
Background Metabolic disorders are associated with increased incidence, aggressive phenotype and poor outcome of breast cancer (BC) patients. For instance, hyperinsulinemia is an independent risk factor for BC and the insulin/insulin receptor (IR) axis is involved in BC growth and metastasis. Of note, the anti-diabetic metformin may be considered in comprehensive therapeutic approaches in BC on the basis of its antiproliferative effects obtained in diverse pre-clinical and clinical studies. Methods Bioinformatics analysis were performed using the information provided by The Invasive Breast Cancer Cohort of The Cancer Genome Atlas (TCGA) project. The naturally immortalized BC cell line, named BCAHC-1, as well as cancer-associated fibroblasts (CAFs) derived from BC patients were used as model systems. In order to identify further mechanisms that characterize the anticancer action of metformin in BC, we performed gene expression and promoter studies as well as western blotting experiments. Moreover, cell cycle analysis, colony and spheroid formation, actin cytoskeleton reorganization, cell migration and matrigel drops evasion assays were carried out to provide novel insights on the anticancer properties of metformin. Results We first assessed that elevated expression and activation of IR correlate with a worse prognostic outcome in estrogen receptor (ER)-positive BC. Thereafter, we established that metformin inhibits the insulin/IR-mediated activation of transduction pathways, gene changes and proliferative responses in BCAHC-1 cells. Then, we found that metformin interferes with the insulin-induced expression of the metastatic gene CXC chemokine receptor 4 (CXCR4), which we found to be associated with poor disease-free survival in BC patients exhibiting high levels of IR. Next, we ascertained that metformin prevents a motile phenotype of BCAHC-1 cells triggered by the paracrine liaison between tumor cells and CAFs upon insulin activated CXCL12/CXCR4 axis. Conclusions Our findings provide novel mechanistic insights regarding the anti-proliferative and anti-migratory effects of metformin in both BC cells and important components of the tumor microenvironment like CAFs. Further investigations are warranted to corroborate the anticancer action of metformin on the tumor mass toward the assessment of more comprehensive strategies halting BC progression, in particular in patients exhibiting metabolic disorders and altered insulin/IR functions. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03463-y.
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24
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Mattorre B, Caristi S, Donato S, Volpe E, Faiella M, Paiardini A, Sorrentino R, Paladini F. A Short ERAP2 That Binds IRAP Is Expressed in Macrophages Independently of Gene Variation. Int J Mol Sci 2022; 23:ijms23094961. [PMID: 35563348 PMCID: PMC9101739 DOI: 10.3390/ijms23094961] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/17/2022] [Accepted: 04/27/2022] [Indexed: 01/19/2023] Open
Abstract
The M1 zinc metalloproteases ERAP1, ERAP2, and IRAP play a role in HLA-I antigen presentation by refining the peptidome either in the ER (ERAP1 and ERAP2) or in the endosomes (IRAP). They have also been entrusted with other, although less defined, functions such as the regulation of the angiotensin system and blood pressure. In humans, ERAP1 and IRAP are commonly expressed. ERAP2 instead has evolved under balancing selection that maintains two haplotypes, one of which undergoing RNA splicing leading to nonsense-mediated decay and loss of protein. Hence, likewise in rodents, wherein the ERAP2 gene is missing, about a quarter of the human population does not express ERAP2. We report here that macrophages, but not monocytes or other mononuclear blood cells, express and secrete an ERAP2 shorter form independent of the haplotype. The generation of this "short" ERAP2 is due to an autocatalytic cleavage within a distinctive structural motif and requires an acidic micro-environment. Remarkably, ERAP2 "short" binds IRAP and the two molecules are co-expressed in the endosomes as well as in the cell membrane. Of note, the same phenomenon could be observed in some cancer cells. These data prompt us to reconsider the role of ERAP2, which might have been maintained in humans due to fulfilling a relevant function in its "short" form.
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Affiliation(s)
- Benedetta Mattorre
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (B.M.); (S.C.); (S.D.); (E.V.); (M.F.)
| | - Silvana Caristi
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (B.M.); (S.C.); (S.D.); (E.V.); (M.F.)
| | - Simona Donato
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (B.M.); (S.C.); (S.D.); (E.V.); (M.F.)
| | - Emilia Volpe
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (B.M.); (S.C.); (S.D.); (E.V.); (M.F.)
| | - Marika Faiella
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (B.M.); (S.C.); (S.D.); (E.V.); (M.F.)
| | - Alessandro Paiardini
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy;
| | - Rosa Sorrentino
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (B.M.); (S.C.); (S.D.); (E.V.); (M.F.)
- Correspondence: (R.S.); (F.P.)
| | - Fabiana Paladini
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (B.M.); (S.C.); (S.D.); (E.V.); (M.F.)
- Correspondence: (R.S.); (F.P.)
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25
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Zarei M, Wang P, Jonveaux J, Haller FM, Gu B, Koulov AV, Jahn M. A novel protocol for in-depth analysis of recombinant adeno-associated virus capsid proteins using UHPLC-MS/MS. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022; 36:e9247. [PMID: 34951071 DOI: 10.1002/rcm.9247] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/16/2021] [Accepted: 12/19/2021] [Indexed: 06/14/2023]
Abstract
RATIONALE In-depth characterization of the three capsid viral proteins (VPs 1, 2, and 3) of adeno-associated viruses (AAVs) is immediately needed to ensure the consistency in gene therapy products and processes. These proteins are typically present at very low concentrations in matrices containing high concentrations of excipients and salts. Thus, there is a need for convenient methods for sample preparation before proteomic analysis. The aim of this study was to meet this need by developing a fast, reliable approach for isolating VPs in a manner enabling their efficient digestion and in-depth characterization using liquid chromatography-mass spectrometry (LC-MS). METHODS VPs from Anc80 were precipitated with different organic solvents, and the resulting precipitates were dissolved in either sodium deoxycholate (SDC) and N-dodecyl-beta-D-maltoside (DDM) or guanidine hydrochloride (Gu-HCl). The peptides obtained by the following enzymatic digestion by either trypsin or Asp-N were analyzed using LC-MS/MS. RESULTS We found that precipitation with chloroform/methanol/water results in fast, efficient preparation of VP samples, allowing 100% and 99.2% amino acid sequence coverage of VP1 for trypsin and Asp-N digestion, respectively. This also allowed complete sequence confirmation of VP1, VP2, and VP3 of Anc80, as well as characterization of the amino acid sequences of the N- and C-terminal regions of each VP, together with their post-translational modifications (PTMs). CONCLUSIONS The presented method enables fast, reliable, and relatively cheap sample preparation for identifying AAV serotypes and characterizing the heterogeneity of capsid viral proteins, including their PTMs.
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Affiliation(s)
| | - Peng Wang
- Lonza Houston, Inc., Houston, Texas, USA
| | | | | | - Bingnan Gu
- Lonza Houston, Inc., Houston, Texas, USA
| | | | - Michael Jahn
- Lonza AG, Drug Product Services, Basel, Switzerland
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26
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Kaya-Zeeb S, Engelmayer L, Straßburger M, Bayer J, Bähre H, Seifert R, Scherf-Clavel O, Thamm M. Octopamine drives honeybee thermogenesis. eLife 2022; 11:74334. [PMID: 35289743 PMCID: PMC8923666 DOI: 10.7554/elife.74334] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/15/2022] [Indexed: 12/13/2022] Open
Abstract
In times of environmental change species have two options to survive: they either relocate to a new habitat or they adapt to the altered environment. Adaptation requires physiological plasticity and provides a selection benefit. In this regard, the Western honeybee (Apis mellifera) protrudes with its thermoregulatory capabilities, which enables a nearly worldwide distribution. Especially in the cold, shivering thermogenesis enables foraging as well as proper brood development and thus survival. In this study, we present octopamine signaling as a neurochemical prerequisite for honeybee thermogenesis: we were able to induce hypothermia by depleting octopamine in the flight muscles. Additionally, we could restore the ability to increase body temperature by administering octopamine. Thus, we conclude that octopamine signaling in the flight muscles is necessary for thermogenesis. Moreover, we show that these effects are mediated by β octopamine receptors. The significance of our results is highlighted by the fact the respective receptor genes underlie enormous selective pressure due to adaptation to cold climates. Finally, octopamine signaling in the service of thermogenesis might be a key strategy to survive in a changing environment.
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Affiliation(s)
- Sinan Kaya-Zeeb
- Behavioral Physiology and Sociobiology, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Lorenz Engelmayer
- Behavioral Physiology and Sociobiology, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Mara Straßburger
- Behavioral Physiology and Sociobiology, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Jasmin Bayer
- Institute for Pharmacy and Food Chemistry, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Heike Bähre
- Institute of Pharmacology, Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Roland Seifert
- Institute of Pharmacology, Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Oliver Scherf-Clavel
- Institute for Pharmacy and Food Chemistry, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Markus Thamm
- Behavioral Physiology and Sociobiology, Julius Maximilian University of Würzburg, Würzburg, Germany
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27
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Balabanova L, Seitkalieva A, Yugay Y, Rusapetova T, Slepchenko L, Podvolotskaya A, Yatsunskaya M, Vasyutkina E, Son O, Tekutyeva L, Shkryl Y. Engineered Fungus Thermothelomyces thermophilus Producing Plant Storage Proteins. J Fungi (Basel) 2022; 8:jof8020119. [PMID: 35205873 PMCID: PMC8877005 DOI: 10.3390/jof8020119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/16/2022] [Accepted: 01/21/2022] [Indexed: 11/30/2022] Open
Abstract
An efficient Agrobacterium-mediated genetic transformation based on the plant binary vector pPZP-RCS2 was carried out for the multiple heterologous protein production in filamentous fungus Thermothelomyces thermophilus F-859 (formerly Myceliophthora thermophila F-859). The engineered fungus Th. thermophilus was able to produce plant storage proteins of Zea mays (α-zein Z19) and Amaranthus hypochondriacus (albumin A1) to enrich fungal biomass by valuable nutritional proteins and improved amino acid content. The mRNA levels of z19 and a1 genes were significantly dependent on their driving promoters: the promoter of tryptophan synthase (PtrpC) was more efficient to express a1, while the promoter of translation elongation factor (Ptef) provided much higher levels of z19 transcript abundance. In general, the total recombinant proteins and amino acid contents were higher in the Ptef-containing clones. This work describes a new strategy to improve mycoprotein nutritive value by overexpression of plant storage proteins.
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Affiliation(s)
- Larissa Balabanova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Prospect 100-letya Vladivostoka 159, 690022 Vladivostok, Russia; (L.B.); (A.S.); (L.S.)
| | - Aleksandra Seitkalieva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Prospect 100-letya Vladivostoka 159, 690022 Vladivostok, Russia; (L.B.); (A.S.); (L.S.)
| | - Yulia Yugay
- Federal Scientific Centre of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Prospect 100-letya Vladivostoka 159, 690022 Vladivostok, Russia; (Y.Y.); (T.R.); (M.Y.); (E.V.)
| | - Tatiana Rusapetova
- Federal Scientific Centre of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Prospect 100-letya Vladivostoka 159, 690022 Vladivostok, Russia; (Y.Y.); (T.R.); (M.Y.); (E.V.)
| | - Lubov Slepchenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Prospect 100-letya Vladivostoka 159, 690022 Vladivostok, Russia; (L.B.); (A.S.); (L.S.)
| | - Anna Podvolotskaya
- Department of Bioeconomy and Food Security, Far Eastern Federal University, B417 Office, Bldg. 20, Ajax St., Russky Island, 690950 Vladivostok, Russia; (A.P.); (O.S.); (L.T.)
- ARNIKA, Territory of PDA Nadezhdinskaya, Centralnay St. 42, 692481 Volno-Nadezhdinskoye, Primorsky Krai, Russia
| | - Margarita Yatsunskaya
- Federal Scientific Centre of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Prospect 100-letya Vladivostoka 159, 690022 Vladivostok, Russia; (Y.Y.); (T.R.); (M.Y.); (E.V.)
| | - Elena Vasyutkina
- Federal Scientific Centre of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Prospect 100-letya Vladivostoka 159, 690022 Vladivostok, Russia; (Y.Y.); (T.R.); (M.Y.); (E.V.)
| | - Oksana Son
- Department of Bioeconomy and Food Security, Far Eastern Federal University, B417 Office, Bldg. 20, Ajax St., Russky Island, 690950 Vladivostok, Russia; (A.P.); (O.S.); (L.T.)
- ARNIKA, Territory of PDA Nadezhdinskaya, Centralnay St. 42, 692481 Volno-Nadezhdinskoye, Primorsky Krai, Russia
| | - Liudmila Tekutyeva
- Department of Bioeconomy and Food Security, Far Eastern Federal University, B417 Office, Bldg. 20, Ajax St., Russky Island, 690950 Vladivostok, Russia; (A.P.); (O.S.); (L.T.)
- ARNIKA, Territory of PDA Nadezhdinskaya, Centralnay St. 42, 692481 Volno-Nadezhdinskoye, Primorsky Krai, Russia
| | - Yury Shkryl
- Federal Scientific Centre of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Prospect 100-letya Vladivostoka 159, 690022 Vladivostok, Russia; (Y.Y.); (T.R.); (M.Y.); (E.V.)
- Correspondence: ; Tel.: +7-4232-312-129; Fax: +7-4232-310-193
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28
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Technique development of high-throughput and high-sensitivity sample preparation and separation for proteomics. Bioanalysis 2021; 14:101-111. [PMID: 34854341 DOI: 10.4155/bio-2021-0202] [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: 11/17/2022] Open
Abstract
Sample preparation and separation methods determine the sensitivity and the quantification accuracy of the proteomics analysis. This article covers a comprehensive review of the recent technique development of high-throughput and high-sensitivity sample preparation and separation methods in proteomics research.
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29
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Ghodasara P, Satake N, Sadowski P, Kopp S, Mills PC. Investigation of cattle plasma proteome in response to pain and inflammation using next generation proteomics technique, SWATH-MS. Mol Omics 2021; 18:133-142. [PMID: 34860232 DOI: 10.1039/d1mo00354b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Pain assessment in farm animals has primarily relied on a combination of behavioral and physiological responses, although these are relatively subjective and difficult to quantify. It is essential to develop more effective biomarkers of pain in production animals since they are frequently exposed to routine surgical husbandry procedures. More effective biomarkers of pain would improve welfare, limit the loss of productivity associated with pain and permit better assessment of analgesics. This study aimed to investigate the use of a modern mass spectrometry data independent acquisition strategy, termed Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS), to detect candidate protein biomarkers that are known to associate with nociceptive and inflammatory processes in cattle, which could then be used to assess the efficacy of potential analgesics. Calves were randomly divided into two groups that were either surgically dehorned or subjected to restraint stress, without provision of anaesthesia or analgesia in accordance with current industry standards. Samples were analysed before and after dehorning at multiple timepoints. Significant changes in protein concentrations were detected predominantly at 24 and 96 h following dehorning, including kininogens, proteins associated with the coagulation and complement cascades and serine protease inhibitors. Gene ontology analysis revealed that the identified candidate biomarkers were associated with stress, wound healing, immune response, blood coagulation and the inflammatory and acute phase responses, which could be expected following surgical damage to tissues, but can now be more objectively assessed. These results offer more definitive and quantitative monitoring of response to tissue injury induced pain and inflammation.
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Affiliation(s)
- Priya Ghodasara
- The University of Queensland, School of Veterinary Science, Gatton, Queensland, Australia.,VIDO-InterVac, University of Saskatchewan, Saskatoon, Canada
| | - Nana Satake
- The University of Queensland, School of Veterinary Science, Gatton, Queensland, Australia.,School of Agriculture and Food Sciences, The University of Queensland, Saint Lucia, Queensland, Australia
| | - Pawel Sadowski
- Central Analytical Research Facility, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Steven Kopp
- The University of Queensland, School of Veterinary Science, Gatton, Queensland, Australia
| | - Paul C Mills
- The University of Queensland, School of Veterinary Science, Gatton, Queensland, Australia
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30
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Zou B, Goodwin M, Saleem D, Jiang W, Tang J, Chu Y, Munford RS, Lu M. A highly conserved host lipase deacylates oxidized phospholipids and ameliorates acute lung injury in mice. eLife 2021; 10:70938. [PMID: 34783310 PMCID: PMC8594946 DOI: 10.7554/elife.70938] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/01/2021] [Indexed: 12/26/2022] Open
Abstract
Oxidized phospholipids have diverse biological activities, many of which can be pathological, yet how they are inactivated in vivo is not fully understood. Here, we present evidence that a highly conserved host lipase, acyloxyacyl hydrolase (AOAH), can play a significant role in reducing the pro-inflammatory activities of two prominent products of phospholipid oxidation, 1-palmitoyl-2-glutaryl-sn-glycero-3-phosphocholine and 1-palmitoyl-2-(5-oxovaleroyl)-sn-glycero-3-phosphocholine. AOAH removed the sn-2 and sn-1 acyl chains from both lipids and reduced their ability to induce macrophage inflammasome activation and cell death in vitro and acute lung injury in mice. In addition to transforming Gram-negative bacterial lipopolysaccharide from stimulus to inhibitor, its most studied activity, AOAH can inactivate these important danger-associated molecular pattern molecules and reduce tissue inflammation and injury.
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Affiliation(s)
- Benkun Zou
- Department of Immunology, Key Laboratory of Medical Molecular Virology (MOE, NHC, CAMS), School of Basic Medical Sciences & Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Michael Goodwin
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, United States
| | - Danial Saleem
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, United States
| | - Wei Jiang
- Department of Immunology, Key Laboratory of Medical Molecular Virology (MOE, NHC, CAMS), School of Basic Medical Sciences & Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Jianguo Tang
- Department of Trauma-Emergency & Critical Care Medicine, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Yiwei Chu
- Department of Immunology, Key Laboratory of Medical Molecular Virology (MOE, NHC, CAMS), School of Basic Medical Sciences & Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Robert S Munford
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, United States
| | - Mingfang Lu
- Department of Immunology, Key Laboratory of Medical Molecular Virology (MOE, NHC, CAMS), School of Basic Medical Sciences & Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.,Department of Trauma-Emergency & Critical Care Medicine, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
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31
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Castaño JD, Zhou M, Schilling J. Towards an Understanding of Oxidative Damage in an α-L-Arabinofuranosidase of Trichoderma reesei: a Molecular Dynamics Approach. Appl Biochem Biotechnol 2021; 193:3287-3300. [PMID: 34125378 DOI: 10.1007/s12010-021-03594-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 05/28/2021] [Indexed: 10/21/2022]
Abstract
Trichoderma reesei is a "workhorse" fungus that produces glycosyl hydrolases (e.g., cellulases) at high titers for use in industrial bioprocessing. In this study, we focused on α-L-arabinofuranosidase, an enzyme important for the treatment of lignocellulosic biomass, but susceptible to oxidative damage that can occur during industrial processing. The molecular details that render this enzyme inactive have not yet been identified. To approach this issue, we used proteomics to identify amino acid residues that were oxidized after a relevant oxidative treatment (Fenton reaction). These oxidative modifications were included in the 3D protein structures, and using molecular dynamics simulations, we then studied the behaviors of non-modified and oxidized enzymes. These simulations showed significant alterations of the conformational stability of the protein when oxidized, as evidenced by changes in root mean square deviation (RMSD) and principal component analyses (PCA) trajectories. Likewise, enzyme-ligand interactions such as hydrogen bonds were greatly reduced in quantity and quality in the oxidized protein. Finally, free energy landscape plots showed that there was a more rugged energy surface in the oxidized protein, implying a less favorable reaction pathway. These results reveal the basis for loss of function in this carbohydrate active enzyme (CAZY) in the commercially relevant fungus T. reesei.
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Affiliation(s)
- Jesus D Castaño
- Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN, 55108, USA
- Marine and Coastal Research Institute, INVEMAR, Santa Marta, Colombia, 470006
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Jonathan Schilling
- Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA.
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32
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Mutavhatsindi H, Calder B, McAnda S, Malherbe ST, Stanley K, Kidd M, Walzl G, Chegou NN. Identification of novel salivary candidate protein biomarkers for tuberculosis diagnosis: A preliminary biomarker discovery study. Tuberculosis (Edinb) 2021; 130:102118. [PMID: 34371310 DOI: 10.1016/j.tube.2021.102118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/28/2021] [Accepted: 08/03/2021] [Indexed: 11/18/2022]
Abstract
BACKGROUND There is an urgent need for new, accurate, rapid, and affordable tuberculosis (TB) diagnostic tests. The aim of the present study was to use mass spectrometry to identify new preliminary candidate TB diagnostic protein biomarkers in saliva obtained from individuals with TB, and patients with other respiratory diseases (ORD). METHODS Saliva samples were collected from 22 individuals who self-presented with symptoms suggestive of TB as part of a larger TB biomarker project. Purified salivary proteins were subjected to tryptic digestion peptides were analyzed using a QExactive Orbitrap Mass Spectrometer. Data are available via ProteomeXchange with identifier PXD027294. Identified proteins were subjected to gene ontology and ingenuity pathway analysis for functional enrichment analysis. RESULTS 26 of the 652 identified proteins significantly discriminated individuals with TB from those with ORD after Benjamini Hochberg correction (5% FDR), with five of these proteins diagnosing TB with an AUC ≥ 0.80. A 5-protein biosignature comprising of P01011, Q8NCW5, P28072, A0A2Q2TTZ9, and Q99574 diagnosed TB with an AUC of 1.00 (95% CI, 1.00-1.00), sensitivity of 100% (95% CI, 76.2-100%) and specificity of 90.9% (95% CI, 58.7-99.8%) after leave-one-out cross validation. CONCLUSIONS We identified novel candidate salivary protein biomarkers and biosignatures with strong potential as TB diagnostic candidates. Our results are preliminary and require validation in larger studies.
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Affiliation(s)
- Hygon Mutavhatsindi
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa.
| | - Bridget Calder
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Shirley McAnda
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa
| | - Stephanus T Malherbe
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa
| | - Kim Stanley
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa
| | - Martin Kidd
- Centre for Statistical Consultation, Department of Statistics and Actuarial Sciences, Stellenbosch University, Cape Town, South Africa
| | - Gerhard Walzl
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa
| | - Novel N Chegou
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa.
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Seddaoui N, Amine A. Smartphone-based competitive immunoassay for quantitative on-site detection of meat adulteration. Talanta 2021; 230:122346. [PMID: 33934795 DOI: 10.1016/j.talanta.2021.122346] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 01/15/2023]
Abstract
Rapid, sensitive, and portable analytical methods for on-site inspection of food fraud are now an urgent requirement to ensure food quality and satisfy the ethnic considerations of consumers. Hence, for the first time, a colorimetric smartphone-based immunoassay was developed for the on-site detection of pork adulteration in meat. In detail, the immunoassay was based on a competitive strategy in which immobilized standard porcine IgG competed with the target porcine IgG extracted in a single step from meat samples. The parameters involved in each step of the immunoassay conception and the digital colorimetric detection were carefully investigated and optimized. Using polystyrene microplates as ready-to-use stable and portable immunoplatforms, TMB as chromogenic substrate, smartphone as signal readout, and Image J software for image processing; the developed immunoassay was able to detect as low as 0.01% of pork in meat mixtures in a total assay time of 30 min. The selectivity of the immunoassay was evaluated for different meat species, and it was shown to selectively respond only to pork. Furthermore, excellent stability of the prepared immunological platform was demonstrated under extreme temperature conditions (50 °C), which confirms its high portability potential for in situ quantification of pork, while being relatively cost effective and non-laborious. The developed method also provides great precision (RSD < 6%) and accuracy (relative error< 6%). Given the universal use of smartphones as portable and affordable devices, such format of immunoassay could be a promising approach for rapid and sensitive real-time monitoring of food fraud.
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Affiliation(s)
- Narjiss Seddaoui
- Laboratory of Process Engineering and Environment, Faculty of Sciences and Techniques, Hassan II University of Casablanca, P.A. 146, Mohammedia, Morocco
| | - Aziz Amine
- Laboratory of Process Engineering and Environment, Faculty of Sciences and Techniques, Hassan II University of Casablanca, P.A. 146, Mohammedia, Morocco.
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Gross LE, Klinger A, Spies N, Ernst T, Flinner N, Simm S, Ladig R, Bodensohn U, Schleiff E. Insertion of plastidic β-barrel proteins into the outer envelopes of plastids involves an intermembrane space intermediate formed with Toc75-V/OEP80. THE PLANT CELL 2021; 33:1657-1681. [PMID: 33624803 PMCID: PMC8254496 DOI: 10.1093/plcell/koab052] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/03/2021] [Indexed: 06/12/2023]
Abstract
The insertion of organellar membrane proteins with the correct topology requires the following: First, the proteins must contain topogenic signals for translocation across and insertion into the membrane. Second, proteinaceous complexes in the cytoplasm, membrane, and lumen of organelles are required to drive this process. Many complexes required for the intracellular distribution of membrane proteins have been described, but the signals and components required for the insertion of plastidic β-barrel-type proteins into the outer membrane are largely unknown. The discovery of common principles is difficult, as only a few plastidic β-barrel proteins exist. Here, we provide evidence that the plastidic outer envelope β-barrel proteins OEP21, OEP24, and OEP37 from pea (Pisum sativum) and Arabidopsis thaliana contain information defining the topology of the protein. The information required for the translocation of pea proteins across the outer envelope membrane is present within the six N-terminal β-strands. This process requires the action of translocon of the outer chloroplast (TOC) membrane. After translocation into the intermembrane space, β-barrel proteins interact with TOC75-V, as exemplified by OEP37 and P39, and are integrated into the membrane. The membrane insertion of plastidic β-barrel proteins is affected by mutation of the last β-strand, suggesting that this strand contributes to the insertion signal. These findings shed light on the elements and complexes involved in plastidic β-barrel protein import.
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Affiliation(s)
- Lucia E Gross
- Department of Molecular Cell Biology of Plants, Goethe University, Max-von-Laue Str. 9; D-60438 Frankfurt, Germany
| | - Anna Klinger
- Department of Molecular Cell Biology of Plants, Goethe University, Max-von-Laue Str. 9; D-60438 Frankfurt, Germany
| | - Nicole Spies
- Department of Molecular Cell Biology of Plants, Goethe University, Max-von-Laue Str. 9; D-60438 Frankfurt, Germany
| | - Theresa Ernst
- Department of Molecular Cell Biology of Plants, Goethe University, Max-von-Laue Str. 9; D-60438 Frankfurt, Germany
| | - Nadine Flinner
- Department of Molecular Cell Biology of Plants, Goethe University, Max-von-Laue Str. 9; D-60438 Frankfurt, Germany
| | - Stefan Simm
- Department of Molecular Cell Biology of Plants, Goethe University, Max-von-Laue Str. 9; D-60438 Frankfurt, Germany
- Frankfurt Institute for Advanced Studies, D-60438 Frankfurt, Germany
| | - Roman Ladig
- Department of Molecular Cell Biology of Plants, Goethe University, Max-von-Laue Str. 9; D-60438 Frankfurt, Germany
| | - Uwe Bodensohn
- Department of Molecular Cell Biology of Plants, Goethe University, Max-von-Laue Str. 9; D-60438 Frankfurt, Germany
| | - Enrico Schleiff
- Department of Molecular Cell Biology of Plants, Goethe University, Max-von-Laue Str. 9; D-60438 Frankfurt, Germany
- Frankfurt Institute for Advanced Studies, D-60438 Frankfurt, Germany
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Sridhar A, Krishnasamy Sekar R, Manikandan DB, Arumugam M, Veeran S, Ramasamy T. Activity profile of innate immune-related enzymes and bactericidal of freshwater fish epidermal mucus extract at different pH. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:33914-33926. [PMID: 33090344 DOI: 10.1007/s11356-020-11173-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
The epidermal mucus of fish performs diverse functions from prevention of mechanical abrasion to limit pathogen invasions. The current experiment was designed to extract skin mucus proteins of three freshwater fish, i.e. common carp (Cyprinus carpio), mrigal (Cirrhinus mrigala) and rohu (Labeo rohita) with organic solvent (methanol) and dissolve in different pH of Tris-HCl buffers to examine the significance of pH in the solubilisation of skin mucus proteins. The protein profiles of different pH solubilised methanol fish skin mucus extracts were determined by SDS-PAGE. The non-specific immune enzymes, alkaline phosphatase, lysozyme and protease of fish skin mucus were compared and this present study demonstrated that these enzymes differed in their activity depending on pH buffers. The higher lysozyme and protease activity were observed at the pH of 8.0 and higher alkaline phosphatase activity in the pH 9.0 of C. mrigala fish skin mucus methanol extract. In addition, the bactericidal activity was evaluated against the pathogens Proteus vulgaris and Pseudomonas aeruginosa. The pH 8.0 of C. mrigala skin mucus extract revealed better bactericidal activity than other fish species mucus pH buffers against both P. vulgaris and P. aeruginosa. In the case of protein profile from SDS-PAGE, based on pH buffers and the solubilisation of proteins, differences in the resolution of bands were observed. The higher alkaline pH of 9.0 showed smeared gel bands in all the three fish skin mucus methanol extract. The present study suggests that methanol extracted C. mrigala fish skin mucus at pH 8.0 showed better innate immune enzymes and bactericidal activity. The additional examinations of C. mrigala skin mucus methanol extract in this pH aids in identifying novel bioactive molecules. This is the study of proteome of three fish species skin mucus in the effect of pH. Further analyses are required to evaluate proteins present in fish skin mucus extracted with methanol and the influence of pH on protein solubility. These findings could be helpful in exploring natural alternatives to antibiotics in aquaculture industry against infectious pathogens.
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Affiliation(s)
- Arun Sridhar
- Laboratory of Aquabiotics/Nanoscience, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620 024, India
| | - Rajkumar Krishnasamy Sekar
- Laboratory of Aquabiotics/Nanoscience, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620 024, India
| | - Dinesh Babu Manikandan
- Laboratory of Aquabiotics/Nanoscience, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620 024, India
| | - Manikandan Arumugam
- Laboratory of Aquabiotics/Nanoscience, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620 024, India
| | - Srinivasan Veeran
- Laboratory of Aquabiotics/Nanoscience, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620 024, India
| | - Thirumurugan Ramasamy
- Laboratory of Aquabiotics/Nanoscience, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620 024, India.
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36
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Extraction of protein from banana by-product and its characterization. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2021. [DOI: 10.1007/s11694-020-00803-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Santolla MF, Talia M, Maggiolini M. S100A4 Is Involved in Stimulatory Effects Elicited by the FGF2/FGFR1 Signaling Pathway in Triple-Negative Breast Cancer (TNBC) Cells. Int J Mol Sci 2021; 22:ijms22094720. [PMID: 33946884 PMCID: PMC8124532 DOI: 10.3390/ijms22094720] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 12/11/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive breast tumor subtype characterized by poor clinical outcome. In recent years, numerous advancements have been made to better understand the biological landscape of TNBC, though appropriate targets still remain to be determined. In the present study, we have determined that the expression levels of FGF2 and S100A4 are higher in TNBC with respect to non-TNBC patients when analyzing “The Invasive Breast Cancer Cohort of The Cancer Genome Atlas” (TCGA) dataset. In addition, we have found that the gene expression of FGF2 is positively correlated with S100A4 in TNBC samples. Performing quantitative PCR, Western blot, CRISPR/Cas9 genome editing, promoter studies, immunofluorescence analysis, subcellular fractionation studies, and ChIP assays, we have also demonstrated that FGF2 induces in TNBC cells the upregulation and secretion of S100A4 via FGFR1, along with the ERK1/2–AKT–c-Rel transduction signaling. Using conditioned medium from TNBC cells stimulated with FGF2, we have also ascertained that the paracrine activation of the S100A4/RAGE pathway triggers angiogenic effects in vascular endothelial cells (HUVECs) and promotes the migration of cancer-associated fibroblasts (CAFs). Collectively, our data provide novel insights into the action of the FGF2/FGFR1 axis through S100A4 toward stimulatory effects elicited in TNBC cells.
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MESH Headings
- Antigens, Neoplasm/physiology
- Cell Movement/drug effects
- Culture Media, Conditioned/pharmacology
- Female
- Fibroblast Growth Factor 2/pharmacology
- Fibroblast Growth Factor 2/physiology
- Fibroblasts/pathology
- Gene Expression Regulation, Neoplastic/physiology
- Human Umbilical Vein Endothelial Cells
- Humans
- Mitogen-Activated Protein Kinases/physiology
- Neoplasm Proteins/physiology
- Neovascularization, Pathologic/physiopathology
- Paracrine Communication
- Protein Kinase Inhibitors/pharmacology
- Proto-Oncogene Proteins c-rel/physiology
- Receptor, Fibroblast Growth Factor, Type 1/antagonists & inhibitors
- Receptor, Fibroblast Growth Factor, Type 1/genetics
- Receptor, Fibroblast Growth Factor, Type 1/physiology
- S100 Calcium-Binding Protein A4/physiology
- Signal Transduction/drug effects
- Signal Transduction/physiology
- Triple Negative Breast Neoplasms/blood supply
- Triple Negative Breast Neoplasms/physiopathology
- Tumor Cells, Cultured
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38
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Alahmad W, Kraiya C, Varanusupakul P, Tabani H, Varanusupakul P. Gel electromembrane microextraction followed by ion chromatography for direct determination of iodine in supplements and fortified food samples: Green chemistry for food analysis. Food Chem 2021; 358:129857. [PMID: 33940293 DOI: 10.1016/j.foodchem.2021.129857] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/13/2021] [Accepted: 04/13/2021] [Indexed: 10/21/2022]
Abstract
In this study, a sensitive, selective, and environmentally friendly analytical method for direct extraction and preconcentration of iodine was developed. Iodine, as an iodate ion or iodide ion, was simultaneously extracted and preconcentrated by gel electromembrane microextraction (G-EME) and analyzed for total iodine by ion chromatography. The total iodine was determined by combining the peak areas of both iodate and iodide ions. Under the optimized conditions, linear calibration for iodine using a mixture of iodate and iodide ions was obtained from 10 to 100 µg L-1 (r2 > 0.996). The detection limit was 7.0 µg L-1. Recoveries of spiked iodine (as iodate) in the samples were greater than 90%. The method was applied for the determination of iodine in dietary supplements and fortified food samples, i.e., iodine-enriched eggs. Our developed method could be directly applied for the determination of iodine in different matrix samples including eggs without a pretreatment step.
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Affiliation(s)
- Waleed Alahmad
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
| | - Charoenkwan Kraiya
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand; Electrochemistry and Optical Spectroscopy Center of Excellence, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | | | - Hadi Tabani
- Department of Environmental Geology, Research Institute of Applied Sciences (ACECR), Shahid Beheshti University, Tehran, Iran
| | - Pakorn Varanusupakul
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
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Methanol Skin Mucus Extract of Mrigal (Cirrhinus mrigala) Fish Peptide Targeting Viral Particles of Infectious Pancreatic Necrosis Virus (IPNV) and Infectious Salmon Anemia Virus (ISAV): an in silico Approach. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10179-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Effect of cross-linked enzyme aggregate strategy on characterization of sn-1,3 extracellular lipase from Aspergillus niger GZUF36. Appl Microbiol Biotechnol 2021; 105:1925-1941. [PMID: 33559718 DOI: 10.1007/s00253-021-11160-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 01/22/2021] [Accepted: 02/02/2021] [Indexed: 10/22/2022]
Abstract
The sn-1,3 extracellular lipase from Aspergillus niger GZUF36 (EXANL1) has important potential applications. The cross-linked enzyme aggregate (CLEA) of purified EXANL1 (CLEA-EXANL1) achieved optimum activity recovery (148.5 ± 0.9%), immobilization yield (100 ± 0%), and recovered activity (99.7 ± 0.6%) with 80% tert-butanol as the precipitant, glutaraldehyde (GA) concentration of 30 mM, GA treatment time of 1.5 h, and centrifugal speed of 6000×g. The effect of CLEA strategy on the characterization of EXANL1 was evaluated in this work. CLEA-EXANL1 exhibited a broader optimum pH range (4-6) compared with free EXANL1 (6.5). CLEA-EXANL1 presented optimum activity at 40 °C, which was 5 °C higher than that of free EXANL1. CLEA strategy decreased the maximum reaction rate and increased the Michaelis-Menten constant of EXANL1 when olive oil emulsion was used as a substrate. Moreover, after 30 days, free EXANL1 lost more than 80.0% of its activity, whereas CLEA-EXANL1 retained more than 90.0% of its activity. CLEA strategy improved the tolerance of EXANL1 in polar organic solvents. Fourier transform infrared spectroscopy results showed that the CLEA technique increased the contents of β-sheets and β-turns in EXANL1 and reduced those of α-helixes and irregular crimps. CLEA strategy caused no change in the sn-1,3 selectivity of EXANL1. Therefore, EXANL1 in the form of CLEA is a valuable catalyst in the synthesis of 1,3-diacylglycerol. KEY POINTS: • Cross-linked enzyme aggregate (CLEA) strategy broadened the optimum pH range of sn-1,3 extracellular lipase from Aspergillus niger GZUF36 (EXANL1). • CLEA strategy improved the tolerance of EXANL1 in polar organic solvents. • CLEA strategy caused no change in the positional selectivity of EXANL1.
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Bose U, Broadbent JA, Juhász A, Karnaneedi S, Johnston EB, Stockwell S, Byrne K, Limviphuvadh V, Maurer-Stroh S, Lopata AL, Colgrave ML. Protein extraction protocols for optimal proteome measurement and arginine kinase quantitation from cricket Acheta domesticus for food safety assessment. Food Chem 2021; 348:129110. [PMID: 33508605 DOI: 10.1016/j.foodchem.2021.129110] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/06/2021] [Accepted: 01/11/2021] [Indexed: 12/20/2022]
Abstract
Insects have been consumed by people for millennia and have recently been proposed as a complementary, sustainable source of protein to feed the world's growing population. Insects and crustaceans both belong to the arthropod family. Crustacean (shellfish) allergies are common and potentially severe; hence, the cross-reactivity of the immune system with insect proteins is a potential health concern. Herein, LC-MS/MS was used to explore the proteome of whole, roasted whole and roasted powdered cricket products. Eight protein extraction protocols were compared using the total number of protein and distinct peptide identifications. Within these data, 20 putative allergens were identified, of which three were arginine kinase (AK) proteoforms. Subsequently, a multiple reaction monitoring MS assay was developed for the AK proteoforms and applied to a subset of extracts. This targeted assay demonstrated that allergen abundance/detectability varies according to the extraction method as well as the food processing method.
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Affiliation(s)
- Utpal Bose
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - James A Broadbent
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Angéla Juhász
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia
| | - Shaymaviswanathan Karnaneedi
- Molecular Allergy Research Laboratory, Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, Australia
| | - Elecia B Johnston
- Molecular Allergy Research Laboratory, Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, Australia
| | - Sally Stockwell
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Keren Byrne
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Vachiranee Limviphuvadh
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore; IFCS Programme, Singapore Institute for Food and Biotechnology Innovation, Agency for Science, Technology and Research, Singapore
| | - Sebastian Maurer-Stroh
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore; IFCS Programme, Singapore Institute for Food and Biotechnology Innovation, Agency for Science, Technology and Research, Singapore; Department of Biological Sciences, National University of Singapore, Singapore
| | - Andreas L Lopata
- Molecular Allergy Research Laboratory, Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, Australia
| | - Michelle L Colgrave
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia.
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Oliveira APD, Naozuka J. Iron species and proteins distribution in unconventional food plants. BRAZILIAN JOURNAL OF FOOD TECHNOLOGY 2021. [DOI: 10.1590/1981-6723.29420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract The sustainable food valorization is capable to stimulate the local products consumption with quality and nutritional security. In this scenario, Unconventional Food Plants (UFPs) deserve attention representing an alternative for rural communities and contributing to the local and regional economy. This work aimed to add nutritional information, once it evaluates total Fe concentration, Fe-species (water soluble, acid soluble, and inorganic), proteins, and Fe- proteins distribution in beldroega (Portulaca oleracea L.), guasca (Galinsoga parviflora Cav.), ora-pro-nóbis (Pereskia aculeata Mill.), piracá (Vernonia scorpioides (Lam.) Pers.), and trapoeraba (Commelina benghalensis L.). Considering the Fe total concentration, the studied UPFs can be excellent Fe sources, when compared to foods of plant origin widely consumed and cultivated, detaching the guasca leaves (687±19 µg g-1). However, the guasca leaves showed low concentration of Fe associated to macromolecules and Fe soluble species (1.6±0.3 µg g-1). These results may justify the low bioavailability of Fe species. On the other hand, beldroega leaves presented the highest concentration of inorganic Fe (1.3±0.2 µg g-1). In the UFPs, there is high glutelins concentration when compared to the other protein groups, meaning that UFPs can be low-cost alternative to supplementing protein intake. Finally, for majority UFPs, except guasca leaves, Fe is mainly associated to albumins, being a good source of bioavailable Fe species.
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Györffy BA, Tóth V, Török G, Gulyássy P, Kovács RÁ, Vadászi H, Micsonai A, Tóth ME, Sántha M, Homolya L, Drahos L, Juhász G, Kékesi KA, Kardos J. Synaptic mitochondrial dysfunction and septin accumulation are linked to complement-mediated synapse loss in an Alzheimer's disease animal model. Cell Mol Life Sci 2020; 77:5243-5258. [PMID: 32034429 PMCID: PMC7671981 DOI: 10.1007/s00018-020-03468-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 12/25/2019] [Accepted: 01/21/2020] [Indexed: 12/21/2022]
Abstract
Synaptic functional disturbances with concomitant synapse loss represent central pathological hallmarks of Alzheimer's disease. Excessive accumulation of cytotoxic amyloid oligomers is widely recognized as a key event that underlies neurodegeneration. Certain complement components are crucial instruments of widespread synapse loss because they can tag synapses with functional impairments leading to their engulfment by microglia. However, an exact understanding of the affected synaptic functions that predispose to complement-mediated synapse elimination is lacking. Therefore, we conducted systematic proteomic examinations on synaptosomes prepared from an amyloidogenic mouse model of Alzheimer's disease (APP/PS1). Synaptic fractions were separated according to the presence of the C1q-tag using fluorescence-activated synaptosome sorting and subjected to proteomic comparisons. The results raised the decline of mitochondrial functions in the C1q-tagged synapses of APP/PS1 mice based on enrichment analyses, which was verified using flow cytometry. Additionally, proteomics results revealed extensive alterations in the level of septin protein family members, which are known to dynamically form highly organized pre- and postsynaptic supramolecular structures, thereby affecting synaptic transmission. High-resolution microscopy investigations demonstrated that synapses with considerable amounts of septin-3 and septin-5 show increased accumulation of C1q in APP/PS1 mice compared to the wild-type ones. Moreover, a strong positive correlation was apparent between synaptic septin-3 levels and C1q deposition as revealed via flow cytometry and confocal microscopy examinations. In sum, our results imply that deterioration of synaptic mitochondrial functions and alterations in the organization of synaptic septins are associated with complement-dependent synapse loss in Alzheimer's disease.
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Affiliation(s)
- Balázs A Györffy
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
- Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Vilmos Tóth
- Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
- Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - György Török
- Molecular Cell Biology Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences Centre of Excellence, Budapest, Hungary
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Péter Gulyássy
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Réka Á Kovács
- Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Henrietta Vadászi
- Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - András Micsonai
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
- Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Melinda E Tóth
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Miklós Sántha
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - László Homolya
- Molecular Cell Biology Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences Centre of Excellence, Budapest, Hungary
| | - László Drahos
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Gábor Juhász
- Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
- CRU Hungary Ltd., Göd, Hungary
| | - Katalin A Kékesi
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
- Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
- Department of Physiology and Neurobiology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - József Kardos
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary.
- Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary.
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Barros PDSD, Silva PECE, Nascimento TP, Costa RMPB, Bezerra RP, Porto ALF. Fibrinolytic enzyme from Arthrospira platensis cultivated in medium culture supplemented with corn steep liquor. Int J Biol Macromol 2020; 164:3446-3453. [DOI: 10.1016/j.ijbiomac.2020.08.217] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 11/26/2022]
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45
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Michaud SA, Pětrošová H, Jackson AM, McGuire JC, Sinclair NJ, Ganguly M, Flenniken AM, Nutter LMJ, McKerlie C, Schibli D, Smith D, Borchers CH. Process and Workflow for Preparation of Disparate Mouse Tissues for Proteomic Analysis. J Proteome Res 2020; 20:305-316. [PMID: 33151080 DOI: 10.1021/acs.jproteome.0c00399] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigated the effect of homogenization strategy and protein precipitation on downstream protein quantitation using multiple reaction monitoring mass spectrometry (MRM-MS). Our objective was to develop a workflow capable of processing disparate tissue types with high throughput, minimal variability, and maximum purity. Similar abundances of endogenous proteins were measured in nine different mouse tissues regardless of the homogenization method used; however, protein precipitation had strong positive effects on several targets. The best throughput was achieved by lyophilizing tissues to dryness, followed by homogenization via bead-beating without sample buffer. Finally, the effect of tissue perfusion prior to dissection and collection was explored in 20 mouse tissues. MRM-MS showed decreased abundances of blood-related proteins in perfused tissues; however, complete removal was not achieved. Concentrations of nonblood proteins were largely unchanged, although significantly higher variances were observed for proteins from the perfused lung, indicating that perfusion may not be suitable for this organ. We present a simple yet effective tissue processing workflow consisting of harvest of fresh nonperfused tissue, novel lyophilization and homogenization by bead-beating, and protein precipitation. This workflow can be applied to a range of mouse tissues with the advantages of simplicity, minimal manual manipulation of samples, use of commonly available equipment, and high sample quality.
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Affiliation(s)
- Sarah A Michaud
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria V8Z 7X8, British Columbia, Canada
| | - Helena Pětrošová
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria V8Z 7X8, British Columbia, Canada
| | - Angela M Jackson
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria V8Z 7X8, British Columbia, Canada
| | - Jamie C McGuire
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria V8Z 7X8, British Columbia, Canada
| | - Nicholas J Sinclair
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria V8Z 7X8, British Columbia, Canada
| | - Milan Ganguly
- The Center for Phenogenomics, Toronto M5T 3H7, Ontario, Canada.,The Hospital for Sick Children, Toronto M5G 1X8, Ontario, Canada
| | - Ann M Flenniken
- The Center for Phenogenomics, Toronto M5T 3H7, Ontario, Canada.,Sinai Health Lunenfeld-Tanenbaum Research Institute, Toronto M5G 1X5, Ontario, Canada
| | - Lauryl M J Nutter
- The Center for Phenogenomics, Toronto M5T 3H7, Ontario, Canada.,The Hospital for Sick Children, Toronto M5G 1X8, Ontario, Canada
| | - Colin McKerlie
- The Center for Phenogenomics, Toronto M5T 3H7, Ontario, Canada.,The Hospital for Sick Children, Toronto M5G 1X8, Ontario, Canada
| | - David Schibli
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria V8Z 7X8, British Columbia, Canada
| | - Derek Smith
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria V8Z 7X8, British Columbia, Canada
| | - Christoph H Borchers
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria V8Z 7X8, British Columbia, Canada.,Department of Data Intensive Science and Engineering, Skolkovo Innovation Center, Skolkovo Institute of Science and Technology, Nobel Street, Moscow 143026, Russia.,Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal H3T 1E2, Quebec, Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal H3T 1E2, Quebec, Canada
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46
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Low YL, Pan Y, Short JL, Nicolazzo JA. Development and validation of a LC-MS/MS assay for quantifying the uptake of docosahexaenoic acid-d5 into mouse microglia. J Pharm Biomed Anal 2020; 191:113575. [DOI: 10.1016/j.jpba.2020.113575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 08/10/2020] [Accepted: 08/12/2020] [Indexed: 02/06/2023]
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47
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Pérez-Rodriguez S, Ramírez OT, Trujillo-Roldán MA, Valdez-Cruz NA. Comparison of protein precipitation methods for sample preparation prior to proteomic analysis of Chinese hamster ovary cell homogenates. ELECTRON J BIOTECHN 2020. [DOI: 10.1016/j.ejbt.2020.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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48
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Zhou L, Zhou M, Gritsenko MA, Stacey G. Selective Enrichment Coupled with Proteomics to Identify S-Acylated Plasma Membrane Proteins in Arabidopsis. ACTA ACUST UNITED AC 2020; 5:e20119. [PMID: 32976704 DOI: 10.1002/cppb.20119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein S-acylation, predominately in the form of palmitoylation, is a reversible lipid post-translational modification on cysteines that plays important roles in protein localization, trafficking, activity, and complex assembly. The functions and regulatory mechanisms of S-acylation have been extensively studied in mammals owing to remarkable development of high-resolution proteomics and the discovery of the S-acylation-related enzymes. However, the advancement of S-acylation studies in plants lags behind that in mammals, mainly due to the lack of knowledge about proteins responsible for this process, such as protein acyltransferases and their substrates. In this article, a set of systematic protocols to study global S-acylation in Arabidopsis seedlings is described. The procedures are presented in detail, including preparation of Arabidopsis seedlings, enrichment of plasma membrane (PM) proteins, ensuing enrichment of S-acylated proteins/peptides based on the acyl-biotin exchange method, and large-scale identification of S-acylated proteins/peptides via mass spectrometry. This approach enables researchers to study S-acylation of PM proteins in plants in a systematic and straightforward way. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Preparation of Arabidopsis seedling materials Basic Protocol 2: Isolation and enrichment of plasma membrane proteins Support Protocol 1: Determination of protein concentration using BCA assay Basic Protocol 3: Enrichment of S-acylated proteins by acyl-biotin exchange method Support Protocol 2: Protein precipitation by methanol/chloroform method Basic Protocol 4: Trypsin digestion and proteomic analysis Alternate Protocol: Pre-resin digestion and peptide-level enrichment.
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Affiliation(s)
- Lijuan Zhou
- Division of Plant Sciences, C.S. Bond Life Science Center, University of Missouri, Columbia, Missouri
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
| | - Marina A Gritsenko
- Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Gary Stacey
- Division of Plant Sciences, C.S. Bond Life Science Center, University of Missouri, Columbia, Missouri.,Division of Biochemistry, C.S. Bond Life Science Center, University of Missouri, Columbia, Missouri
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49
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Maryam Ghafari S, Ebrahimi S, Nateghi Rostami M, Bordbar A, Parvizi P. Comparative evaluation of salivary glands proteomes from wild Phlebotomus papatasi-proven vector of zoonotic cutaneous leishmaniasis in Iran. Vet Med Sci 2020; 7:362-369. [PMID: 32969601 PMCID: PMC8025609 DOI: 10.1002/vms3.368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/01/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Zoonotic Cutaneous Leishmaniasis is increasing in the world and Phlebotomus papatasi as a proven vector was considered in different aspects for disease control. Sandfly saliva contains proteins which provoke host immune system. These proteins are candidates for developing vaccines. OBJECTIVES The main purpose of this research was comparing evaluation of salivary glands proteomes from wild P. papatasi. Extracting these proteins and purifying of original SP15 as inducer agent in vector salivary glands from endemic leishmaniasis foci were other objectives. METHODS Adult sandflies were sampled using aspirators and funnel traps from three endemic foci in 2017-2018. Each pair of salivary glands of unfed females was dissected and proteins were extracted using thermal shocking and sonication methods. Purification was performed through RP-HPLC. All equivalent fractions were added together in order to reach sufficient protein concentration. Protein content and profile determination were examined with SDS-PAGE. RESULTS The protein concentration of whole-salivary glands of specimens was determined approximately 1.6 µg/µl (Isfahan) and 1 µg/µl (Varamin and Kashan). SDS-PAGE revealed 10 distinct bands between 10 and 63 kDa. Analysis of proteomes showed some similarities and differences in the chromatograms of different foci. SDS-PAGE of all collected fractions revealed SP15-like proteins were isolated in 24 min from Varamin, 26 to 30 min from Kashan and 29.4 min from Isfahan and were around 15 kDa. CONCLUSIONS Isolation of salivary components of Iranian wild P. papatasi is very important for finding potential proteins in vaccine development and measuring control strategy of zoonotic cutaneous leishmaniasis in Iran and this could be concluded elsewhere in the world.
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Affiliation(s)
- Seyedeh Maryam Ghafari
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, Tehran, Iran
| | - Sahar Ebrahimi
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, Tehran, Iran
| | | | - Ali Bordbar
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, Tehran, Iran
| | - Parviz Parvizi
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, Tehran, Iran
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Licini C, Montalbano G, Ciapetti G, Cerqueni G, Vitale-Brovarone C, Mattioli-Belmonte M. Analysis of multiple protein detection methods in human osteoporotic bone extracellular matrix: From literature to practice. Bone 2020; 137:115363. [PMID: 32298836 DOI: 10.1016/j.bone.2020.115363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/02/2020] [Accepted: 04/07/2020] [Indexed: 11/15/2022]
Abstract
The punctual analysis of bone Extracellular Matrix (ECM) proteins represents a pivotal point for medical research in bone diseases like osteoporosis. Studies in this field, historically done to appreciate bone biology, were mainly conducted on animal samples and, up to today, only a few studies on protein detection in human bone are present. The challenges in bone ECM protein extraction and quantitation protocols are related to both the separation of proteins from the mineral content (i.e. hydroxyapatite) and the difficulty of avoiding protein denaturation during the extraction processes. The aim of the present work was to define appropriate protocol(s) for bone ECM protein extraction that could be applied to investigate both normal and pathological conditions. We compared and optimised some of the most used protocols present in the literature, modifying the protein precipitation method, the buffer used for resuspension and/or the volume of reagent used. Bradford and BCA assays and Western Blotting were used to evaluate the variations in the total protein recovery and the amount of selected proteins (Type I Collagen, TGF-β, IGF-1, Decorin, Osteopontin, Bone Sialoprotein-2 and Osteocalcin). Collectively, we were capable to draw-up two single-extract protocols with optimal recovery and ideal protein content, that can be used for a detailed analysis of ECM proteins in pathological bone samples. Time-consuming multi-extract procedures, optimised in their precipitation methods, are however crucial for a precise detection of specific proteins, like osteocalcin. As the matter of fact, also the demineralization processes, commonly suggested and performed in several protocols, could hinder an accurate protein detection, thus inherently affecting the study of a pathological bone ECM. This study represents a starting point for the definition of appropriate strategies in the study of bone extracellular matrix proteins involved in the onset and maintenance of bone diseases, as well as a tool for the development of customized scaffolds capable to modulate a proper feedback loop in bone remodelling, altered in case of diseases like osteoporosis.
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Affiliation(s)
- Caterina Licini
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; Department of Clinical and Molecular Sciences (DISCLIMO), Università Politecnica delle Marche, Via Tronto 10/A, 60126 Ancona, Italy
| | - Giorgia Montalbano
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Gabriela Ciapetti
- Laboratorio di Fisiopatologia Ortopedica e Medicina Rigenerativa, Istituto Ortopedico Rizzoli, IRCCS, Via di Barbiano 1/10, 40136 Bologna, Italy
| | - Giorgia Cerqueni
- Department of Clinical and Molecular Sciences (DISCLIMO), Università Politecnica delle Marche, Via Tronto 10/A, 60126 Ancona, Italy
| | - Chiara Vitale-Brovarone
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy.
| | - Monica Mattioli-Belmonte
- Department of Clinical and Molecular Sciences (DISCLIMO), Università Politecnica delle Marche, Via Tronto 10/A, 60126 Ancona, Italy
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