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Serafimov K, Knappe C, Li F, Sievers-Engler A, Lämmerhofer M. Solving the retention time repeatability problem of hydrophilic interaction liquid chromatography. J Chromatogr A 2024; 1730:465060. [PMID: 38861823 DOI: 10.1016/j.chroma.2024.465060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/05/2024] [Accepted: 06/07/2024] [Indexed: 06/13/2024]
Abstract
Hydrophilic interaction (liquid) chromatography (HILIC) has become the first choice LC mode for the separation of hydrophilic analytes. Numerous studies reported the poor retention time repeatability of HILIC. The problem was often ascribed to slow equilibration and insufficient re-equilibration time to establish the sensitive semi-immobilized water layer at the interface of the polar stationary phase and the bulk mobile phase. In this study, we compare retention time repeatability in HILIC for borosilicate glass and PFA (co-polymer of tetrafluoroethylene and perfluoroalkoxyethylene) solvent bottles. During this study, we observed peak patterns shifting towards higher retention times (for metabolites and peptides) and lower retention times (oligonucleotide sample) with ongoing analysis time when standard borosilicate glass bottles were used as solvent reservoirs. It was hypothesized that release of ions (sodium, potassium, borate, etc.) from the borosilicate glass bottles leads to alterations (thickness and electrostatic screening effects) in the semi-immobilized water layer which is adsorbed to the polar stationary phase surface under acetonitrile-rich eluents in HILIC with concomitant shifts in retention. When PFA solvent bottles were employed instead of borosilicate glass, retention time repeatability was greatly improved and changed from average 8.4 % RSD for the tested metabolites with borosilicate glass bottles to 0.14 % RSD for the PFA solvent bottles (30 injections over 12 h). Similar improvements were observed for peptides and oligonucleotides. This simple solution to the retention time repeatability problem in HILIC might contribute to a better acceptance of HILIC, especially in fields like targeted and untargeted metabolomics, peptide and oligonucleotide analysis.
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Affiliation(s)
- Kristian Serafimov
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Cornelius Knappe
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Feiyang Li
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Adrian Sievers-Engler
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
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2
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Gu K, Kumabe H, Yamamoto T, Tashiro N, Masuda T, Ito S, Ohtsuki S. Improving Proteomic Identification Using Narrow Isolation Windows with Zeno SWATH Data-Independent Acquisition. J Proteome Res 2024; 23:3484-3495. [PMID: 38978496 DOI: 10.1021/acs.jproteome.4c00149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Data-independent acquisition (DIA) techniques such as sequential window acquisition of all theoretical mass spectra (SWATH) acquisition have emerged as the preferred strategies for proteomic analyses. Our study optimized the SWATH-DIA method using a narrow isolation window placement approach, improving its proteomic performance. We optimized the acquisition parameter combinations of narrow isolation windows with different widths (1.9 and 2.9 Da) on a ZenoTOF 7600 (Sciex); the acquired data were analyzed using DIA-NN (version 1.8.1). Narrow SWATH (nSWATH) identified 5916 and 7719 protein groups on the digested peptides, corresponding to 400 ng of protein from mouse liver and HEK293T cells, respectively, improving identification by 7.52 and 4.99%, respectively, compared to conventional SWATH. The median coefficient of variation of the quantified values was less than 6%. We further analyzed 200 ng of benchmark samples comprising peptides from known ratios ofEscherichia coli, yeast, and human peptides using nSWATH. Consequently, it achieved accuracy and precision comparable to those of conventional SWATH, identifying an average of 95,456 precursors and 9342 protein groups across three benchmark samples, representing 12.6 and 9.63% improved identification compared to conventional SWATH. The nSWATH method improved identification at various loading amounts of benchmark samples, identifying 40.7% more protein groups at 25 ng. These results demonstrate the improved performance of nSWATH, contributing to the acquisition of deeper proteomic data from complex biological samples.
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Affiliation(s)
- Kongxin Gu
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Haruka Kumabe
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Takumi Yamamoto
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Naoto Tashiro
- Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Takeshi Masuda
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihoji, Tsuruoka, Yamagata 997-0017, Japan
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Shingo Ito
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Sumio Ohtsuki
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
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3
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Przewocki J, Kossiński D, Łukaszuk A, Jakiel G, Wocławek-Potocka I, Ołdziej S, Łukaszuk K. Follicular Fluid Proteomic Analysis to Identify Predictive Markers of Normal Embryonic Development. Int J Mol Sci 2024; 25:8431. [PMID: 39126000 PMCID: PMC11313438 DOI: 10.3390/ijms25158431] [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: 07/01/2024] [Revised: 07/22/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024] Open
Abstract
Ageing populations, mass "baby-free" policies and children born to mothers at the age at which they are biologically expected to become grandmothers are growing problems in most developed societies. Therefore, any opportunity to improve the quality of infertility treatments seems important for the survival of societies. The possibility of indirectly studying the quality of developing oocytes by examining their follicular fluids (hFFs) offers new opportunities for progress in our understanding the processes of final oocyte maturation and, consequently, for predicting the quality of the resulting embryos and personalising their culture. Using mass spectrometry, we studied follicular fluids collected individually during in vitro fertilisation and compared their composition with the quality of the resulting embryos. We analysed 110 follicular fluids from 50 oocyte donors, from which we obtained 44 high-quality, 39 medium-quality, and 27 low-quality embryos. We identified 2182 proteins by Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH-MS) using a TripleTOF 5600+ hybrid mass spectrometer, of which 484 were suitable for quantification. We were able to identify several proteins whose concentrations varied between the follicular fluids of different oocytes from the same patient and between patients. Among them, the most important appear to be immunoglobulin heavy constant alpha 1 (IgA1hc) and dickkopf-related protein 3. The first one is found at higher concentrations in hFFs from which oocytes develop into poor-quality embryos, the other one exhibits the opposite pattern. None of these have, so far, had any specific links to fertility disorders. In light of these findings, these proteins should be considered a primary target for research aimed at developing a diagnostic tool for oocyte quality control and pre-fertilisation screening. This is particularly important in cases where the fertilisation of each egg is not an option for ethical or other reasons, or in countries where it is prohibited by law.
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Affiliation(s)
- Janusz Przewocki
- Institute of Mathematics, University of Gdansk, 80-308 Gdańsk, Poland
- iYoni App—For Fertility Treatment, LifeBite, 10-763 Olsztyn, Poland; (D.K.); (K.Ł.)
| | - Dominik Kossiński
- iYoni App—For Fertility Treatment, LifeBite, 10-763 Olsztyn, Poland; (D.K.); (K.Ł.)
| | - Adam Łukaszuk
- Edinburgh Medical School, College of Medicine and Veterinary Medicine, The University of Edinburgh, 47 Little France Crescent, Edinburgh EH25 9RG, UK
| | - Grzegorz Jakiel
- Invicta Research and Development Center, 81-740 Sopot, Poland
- First Department of Obstetrics and Gynaecology, Centre of Postgraduate Medical Education, 01-004 Warsaw, Poland
| | - Izabela Wocławek-Potocka
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, 10-748 Olsztyn, Poland;
| | - Stanisław Ołdziej
- Intercollegiate Faculty of Biotechnology UG & MUG, University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland;
| | - Krzysztof Łukaszuk
- iYoni App—For Fertility Treatment, LifeBite, 10-763 Olsztyn, Poland; (D.K.); (K.Ł.)
- Department of Obstetrics and Gynecology Nursing, Medical University of Gdańsk, 80-210 Gdańsk, Poland
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Shi J, Liu Y, Xu YJ. MS based foodomics: An edge tool integrated metabolomics and proteomics for food science. Food Chem 2024; 446:138852. [PMID: 38428078 DOI: 10.1016/j.foodchem.2024.138852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/05/2024] [Accepted: 02/24/2024] [Indexed: 03/03/2024]
Abstract
Foodomics has become a popular methodology in food science studies. Mass spectrometry (MS) based metabolomics and proteomics analysis played indispensable roles in foodomics research. So far, several methodologies have been developed to detect the metabolites and proteins in diets and consumers, including sample preparation, MS data acquisition, annotation and interpretation. Moreover, multiomics analysis integrated metabolomics and proteomics have received considerable attentions in the field of food safety and nutrition, because of more comprehensive and deeply. In this context, we intended to review the emerging strategies and their applications in MS-based foodomics, as well as future challenges and trends. The principle and application of multiomics were also discussed, such as the optimization of data acquisition, development of analysis algorithm and exploration of systems biology.
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Affiliation(s)
- Jiachen Shi
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China.
| | - Yuanfa Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China.
| | - Yong-Jiang Xu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China.
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James C, Möller U, Spillner C, König S, Dybkov O, Urlaub H, Lenz C, Kehlenbach RH. Phosphorylation of ELYS promotes its interaction with VAPB at decondensing chromosomes during mitosis. EMBO Rep 2024; 25:2391-2417. [PMID: 38605278 PMCID: PMC11094025 DOI: 10.1038/s44319-024-00125-6] [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: 09/15/2023] [Revised: 02/23/2024] [Accepted: 03/11/2024] [Indexed: 04/13/2024] Open
Abstract
ELYS is a nucleoporin that localizes to the nuclear side of the nuclear pore complex (NPC) in interphase cells. In mitosis, it serves as an assembly platform that interacts with chromatin and then with nucleoporin subcomplexes to initiate post-mitotic NPC assembly. Here we identify ELYS as a major binding partner of the membrane protein VAPB during mitosis. In mitosis, ELYS becomes phosphorylated at many sites, including a predicted FFAT (two phenylalanines in an acidic tract) motif, which mediates interaction with the MSP (major sperm protein)-domain of VAPB. Binding assays using recombinant proteins or cell lysates and co-immunoprecipitation experiments show that VAPB binds the FFAT motif of ELYS in a phosphorylation-dependent manner. In anaphase, the two proteins co-localize to the non-core region of the newly forming nuclear envelope. Depletion of VAPB results in prolonged mitosis, slow progression from meta- to anaphase and in chromosome segregation defects. Together, our results suggest a role of VAPB in mitosis upon recruitment to or release from ELYS at the non-core region of the chromatin in a phosphorylation-dependent manner.
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Affiliation(s)
- Christina James
- Department of Molecular Biology, Faculty of Medicine, GZMB, Georg-August-University Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Ulrike Möller
- Department of Molecular Biology, Faculty of Medicine, GZMB, Georg-August-University Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Christiane Spillner
- Department of Molecular Biology, Faculty of Medicine, GZMB, Georg-August-University Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Sabine König
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, 37075, Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Olexandr Dybkov
- Bioanalytical Mass Spectrometry Group, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, 37075, Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Christof Lenz
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, 37075, Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Ralph H Kehlenbach
- Department of Molecular Biology, Faculty of Medicine, GZMB, Georg-August-University Göttingen, Humboldtallee 23, 37073, Göttingen, Germany.
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6
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Carmona A, Carboni E, Gomes LC, Roudeau S, Maass F, Lenz C, Ortega R, Lingor P. Metal dyshomeostasis in the substantia nigra of patients with Parkinson's disease or multiple sclerosis. J Neurochem 2024; 168:128-141. [PMID: 38178798 DOI: 10.1111/jnc.16040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/12/2023] [Accepted: 12/04/2023] [Indexed: 01/06/2024]
Abstract
Abnormal metal distribution in vulnerable brain regions is involved in the pathogenesis of most neurodegenerative diseases, suggesting common molecular mechanisms of metal dyshomeostasis. This study aimed to compare the intra- and extra-neuronal metal content and the expression of proteins related to metal homeostasis in the substantia nigra (SN) from patients with Parkinson's disease (PD), multiple sclerosis (MS), and control subjects. Metal quantification was performed via ion-beam micro-analysis in neuromelanin-positive neurons and the surrounding tissue. For proteomic analysis, SN tissue lysates were analyzed on a nanoflow chromatography system hyphenated to a hybrid triple-quadrupole time-of-flight mass spectrometer. We found increased amounts of iron in neuromelanin-positive neurons and surrounding tissue in patients with PD and MS compared to controls (4- to 5-fold higher) that, however, also showed large inter-individual variations. Copper content was systematically lower (-2.4-fold) in neuromelanin-positive neurons of PD patients compared with controls, whereas it remained unchanged in MS. Protein-protein interaction (PPI) network analyses revealed clusters related to Fe and Cu homeostasis among PD-deregulated proteins. An enrichment for the term "metal homeostasis" was observed for MS-deregulated proteins. Important deregulated hub proteins included hemopexin and transferrin in PD, and calreticulin and ferredoxin reductase in MS. Our findings show that PD and MS share commonalities in terms of iron accumulation in the SN. Concomitant proteomics experiments revealed PPI networks related to metal homeostasis, substantiating the results of metal quantification.
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Affiliation(s)
| | - Eleonora Carboni
- Department of Neurology, University Medical Center Göttingen, Göttingen, Lower-Saxony, Germany
| | - Lucas Caldi Gomes
- School of Medicine, Klinikum rechts der Isar, Department of Neurology, Technical University of Munich, München, Bavaria, Germany
| | | | - Fabian Maass
- Department of Neurology, University Medical Center Göttingen, Göttingen, Lower-Saxony, Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | | | - Paul Lingor
- School of Medicine, Klinikum rechts der Isar, Department of Neurology, Technical University of Munich, München, Bavaria, Germany
- DZNE, German Center for Neurodegenerative Diseases, Research Site Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
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7
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Schulze B, Heffernan AL, Gomez Ramos MJ, Thomas KV, Kaserzon SL. Influence of extraction windows for data-independent acquisition on feature annotation during suspect screening. CHEMOSPHERE 2024; 349:140697. [PMID: 37972864 DOI: 10.1016/j.chemosphere.2023.140697] [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: 07/12/2023] [Revised: 10/08/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
Non-target analysis (NTA) using high-resolution mass spectrometry is becoming a useful approach to screen for suspect and unknown chemicals. For comprehensive analyses, data-independent acquisition (DIA), like Sequential Windowed Acquisition of all THeoretical Mass Spectra (SWATH-MS) on Sciex instruments, is necessary, usually followed by library matching for feature annotation. The choice of parameters, such as acquisition window number and size, may influence the comprehensiveness of the suspect features detected. The goal of this study was to assess how mass spectrometric DIA settings may influence the ability to obtain confident annotations and identifications of features in environmental (river water, passive sample extract (PSE)), wastewater (unpreserved and acidified) and biological (urine) sample matrices. Each matrix was analysed using 11 different MS methods, with 5-15 variable size acquisition windows. True positive (TP) annotation (i.e., matching experimental and library spectra) rates were constant for PSE (40%) and highest for urine (18%), wastewater (34% and 36%, unpreserved and acidified, respectively) and river water (8%) when using higher numbers of windows (15). The number of annotated features was highest for PSE (12%) and urine (8.5%) when using more acquisition windows (9 and 14, respectively). Less complex matrices (based on average total ion chromatogram intensities) like river water, unpreserved and acidified wastewater have higher annotation rates (7.5%, 8% and 13.2%, respectively) when using less acquisition windows (5-6), indicating matrix dependency of optimum settings. Library scores varied widely for correct (scores between 6 and 100) as well as incorrect annotations (scores between 2 and 100), making it hard to define specific ideal cut-off values. Results highlight the need for properly curated libraries and careful optimization of SWATH-MS and other DIA methods for each individual matrix, finding the best ratio of total annotations to true positive, (i.e., correct) annotations to achieve best NTA results.
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Affiliation(s)
- Bastian Schulze
- The University of Queensland, Queensland Alliance for Environmental Health Sciences (QAEHS), 20 Cornwall Street, Woolloongabba, QLD, 4102, Australia.
| | - Amy L Heffernan
- The University of Queensland, Queensland Alliance for Environmental Health Sciences (QAEHS), 20 Cornwall Street, Woolloongabba, QLD, 4102, Australia
| | - Maria Jose Gomez Ramos
- Chemistry and Physics Department, University of Almeria, Agrifood Campus of International Excellence (ceiA3), 04120, Almería, Spain
| | - Kevin V Thomas
- The University of Queensland, Queensland Alliance for Environmental Health Sciences (QAEHS), 20 Cornwall Street, Woolloongabba, QLD, 4102, Australia
| | - Sarit L Kaserzon
- The University of Queensland, Queensland Alliance for Environmental Health Sciences (QAEHS), 20 Cornwall Street, Woolloongabba, QLD, 4102, Australia
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8
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El-Sayed ASA, Shindia A, Ammar H, Seadawy MG, Khashana SA. Bioprocessing of Epothilone B from Aspergillus fumigatus under solid state fermentation: Antiproliferative activity, tubulin polymerization and cell cycle analysis. BMC Microbiol 2024; 24:43. [PMID: 38291363 PMCID: PMC10829302 DOI: 10.1186/s12866-024-03184-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: 10/07/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024] Open
Abstract
Epothilone derivatives have been recognized as one of the most powerful anticancer drugs towards solid tumors, for their unique affinity to bind with β-tubulin microtubule arrays, stabilizing their disassembly, causing cell death. Sornagium cellulosum is the main source for Epothilone, however, the fermentation bioprocessing of this myxobacteria is the main challenge for commercial production of Epothilone. The metabolic biosynthetic potency of epothilone by Aspergillus fumigatus, an endophyte of Catharanthus roseus, raises the hope for commercial epothilone production, for their fast growth rate and feasibility of manipulating their secondary metabolites. Thus, nutritional optimization of A. fumigatus for maximizing their epothilone productivity under solid state fermentation process is the objective. The highest yield of epothilone was obtained by growing A. fumigatus on orange peels under solid state fermentation (2.2 μg/g), bioprocessed by the Plackett-Burman design. The chemical structure of the extracted epothilone was resolved from the HPLC and LC-MS/MS analysis, with molecular mass 507.2 m/z and identical molecular fragmentation pattern of epothilone B of S. cellulosum. The purified A. fumigatus epothilone had a significant activity towards HepG2 (IC50 0.98 μg/ml), Pancl (IC50 1.5 μg/ml), MCF7 (IC50 3.7 μg/ml) and WI38 (IC50 4.6 μg/ml), as well as a strong anti-tubulin polymerization activity (IC50 0.52 μg/ml) compared to Paclitaxel (2.0 μg/ml). The effect of A. fumigatus epothilone on the immigration ability of HepG2 cells was assessed, as revealed from the wound closure of the monolayer cells that was estimated by ~ 63.7 and 72.5%, in response to the sample and doxorubicin, respectively, compared to negative control. From the Annexin V-PI flow cytometry results, a significant shift of the normal cells to the apoptosis was observed in response to A. fumigatus epothilone by ~ 20 folds compared to control cells, with the highest growth arrest of the HepG2 cells at the G0-G1 stage.
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Affiliation(s)
- Ashraf S A El-Sayed
- Enzymology and Fungal Biotechnology lab, Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt.
| | - Ahmed Shindia
- Enzymology and Fungal Biotechnology lab, Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
| | - Hala Ammar
- Enzymology and Fungal Biotechnology lab, Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
| | - Mohamed G Seadawy
- Biological Prevention Department, Egyptian Ministry of Defense, Cairo, Egypt
| | - Samar A Khashana
- Enzymology and Fungal Biotechnology lab, Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
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9
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Shi J, Zhao J, Zhang Y, Wang Y, Tan CP, Xu YJ, Liu Y. Windows Scanning Multiomics: Integrated Metabolomics and Proteomics. Anal Chem 2023; 95:18793-18802. [PMID: 38095040 DOI: 10.1021/acs.analchem.3c03785] [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: 12/27/2023]
Abstract
Metabolomics and proteomics offer significant advantages in understanding biological mechanisms at two hierarchical levels. However, conventional single omics analysis faces challenges due to the high demand for specimens and the complexity of intrinsic associations. To obtain comprehensive and accurate system biological information, we developed a multiomics analytical method called Windows Scanning Multiomics (WSM). In this method, we performed simultaneous extraction of metabolites and proteins from the same sample, resulting in a 10% increase in the coverage of the identified biomolecules. Both metabolomics and proteomics analyses were conducted by using ultrahigh-performance liquid chromatography mass spectrometry (UPLC-MS), eliminating the need for instrument conversions. Additionally, we designed an R-based program (WSM.R) to integrate mathematical and biological correlations between metabolites and proteins into a correlation network. The network created from simultaneously extracted biomolecules was more focused and comprehensive compared to those from separate extractions. Notably, we excluded six pairs of false-positive relationships between metabolites and proteins in the network established using simultaneously extracted biomolecules. In conclusion, this study introduces a novel approach for multiomics analysis and data processing that greatly aids in bioinformation mining from multiomics results. This method is poised to play an indispensable role in systems biology research.
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Affiliation(s)
- Jiachen Shi
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Jialiang Zhao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Yu Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Yanan Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Chin Ping Tan
- Department of Food Technology, Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Yong-Jiang Xu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Yuanfa Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
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10
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Felgines L, Rymen B, Martins LM, Xu G, Matteoli C, Himber C, Zhou M, Eis J, Coruh C, Böhrer M, Kuhn L, Chicher J, Pandey V, Hammann P, Wohlschlegel J, Waltz F, Law JA, Blevins T. CLSY docking to Pol IV requires a conserved domain critical for small RNA biogenesis and transposon silencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.26.573199. [PMID: 38234754 PMCID: PMC10793415 DOI: 10.1101/2023.12.26.573199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Eukaryotes must balance the need for gene transcription by RNA polymerase II (Pol II) against the danger of mutations caused by transposable element (TE) proliferation. In plants, these gene expression and TE silencing activities are divided between different RNA polymerases. Specifically, RNA polymerase IV (Pol IV), which evolved from Pol II, transcribes TEs to generate small interfering RNAs (siRNAs) that guide DNA methylation and block TE transcription by Pol II. While the Pol IV complex is recruited to TEs via SNF2-like CLASSY (CLSY) proteins, how Pol IV partners with the CLSYs remains unknown. Here we identified a conserved CYC-YPMF motif that is specific to Pol IV and is positioned on the complex exterior. Furthermore, we found that this motif is essential for the co-purification of all four CLSYs with Pol IV, but that only one CLSY is present in any given Pol IV complex. These findings support a "one CLSY per Pol IV" model where the CYC-YPMF motif acts as a CLSY-docking site. Indeed, mutations in and around this motif phenocopy pol iv null mutants. Together, these findings provide structural and functional insights into a critical protein feature that distinguishes Pol IV from other RNA polymerases, allowing it to promote genome stability by targeting TEs for silencing.
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11
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Rady AM, El-Sayed ASA, El-Baz AF, Abdel-Fattah GG, Magdeldin S, Ahmed E, Osama A, Hassanein SE, Saed H, Yassin M. Proteomics and metabolomics analyses of camptothecin-producing Aspergillus terreus reveal the integration of PH domain-containing proteins and peptidylprolyl cis/trans isomerase in restoring the camptothecin biosynthesis. Microbiol Spectr 2023; 11:e0228123. [PMID: 37855596 PMCID: PMC10714794 DOI: 10.1128/spectrum.02281-23] [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: 05/31/2023] [Accepted: 09/25/2023] [Indexed: 10/20/2023] Open
Abstract
IMPORTANCE Decreasing the camptothecin productivity by fungi with storage and subculturing is the challenge that halts their further implementation to be an industrial platform for camptothecin (CPT) production. The highest differentially abundant proteins were Pleckstrin homology (PH) domain-containing proteins and Peptidyl-prolyl cis/trans isomerase that fluctuated with the subculturing of A. terreus with a remarkable relation to CPT biosynthesis and restored with addition of F. elastica microbiome.
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Affiliation(s)
- Amgad M. Rady
- Enzymology and Fungal Biotechnology Lab (EFBL), Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, Egypt
- Faculty of Biotechnology, October University for Modern Sciences and Arts, Giza, Egypt
| | - Ashraf S. A. El-Sayed
- Enzymology and Fungal Biotechnology Lab (EFBL), Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, Egypt
| | - Ashraf F. El-Baz
- Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
| | | | - Sameh Magdeldin
- Proteomics and Metabolomics Research Program, Department of Basic Research, Children’s Cancer Hospital, Cairo, Egypt
- Department of Physiology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Eman Ahmed
- Proteomics and Metabolomics Research Program, Department of Basic Research, Children’s Cancer Hospital, Cairo, Egypt
- Department of Pharmacology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Aya Osama
- Proteomics and Metabolomics Research Program, Department of Basic Research, Children’s Cancer Hospital, Cairo, Egypt
| | - Sameh E. Hassanein
- Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center, Cairo, Egypt
| | - Hend Saed
- Microbiology Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Marwa Yassin
- Enzymology and Fungal Biotechnology Lab (EFBL), Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, Egypt
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12
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Chang JK, Teo G, Pewzner-Jung Y, Cuthbertson DJ, Futerman AH, Wenk MR, Choi H, Torta F. Q-RAI data-independent acquisition for lipidomic quantitative profiling. Sci Rep 2023; 13:19281. [PMID: 37935746 PMCID: PMC10630469 DOI: 10.1038/s41598-023-46312-8] [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: 01/31/2023] [Accepted: 10/30/2023] [Indexed: 11/09/2023] Open
Abstract
Untargeted lipidomics has been increasingly adopted for hypothesis generation in a biological context or discovery of disease biomarkers. Most of the current liquid chromatography mass spectrometry (LC-MS) based untargeted methodologies utilize a data dependent acquisition (DDA) approach in pooled samples for identification and MS-only acquisition for semi-quantification in individual samples. In this study, we present for the first time an untargeted lipidomic workflow that makes use of the newly implemented Quadrupole Resolved All-Ions (Q-RAI) acquisition function on the Agilent 6546 quadrupole time-of-flight (Q-TOF) mass spectrometer to acquire MS2 spectra in data independent acquisition (DIA) mode. This is followed by data processing and analysis on MetaboKit, a software enabling DDA-based spectral library construction and extraction of MS1 and MS2 peak areas, for reproducible identification and quantification of lipids in DIA analysis. This workflow was tested on lipid extracts from human plasma and showed quantification at MS1 and MS2 levels comparable to multiple reaction monitoring (MRM) targeted analysis of the same samples. Analysis of serum from Ceramide Synthase 2 (CerS2) null mice using the Q-RAI DIA workflow identified 88 lipid species significantly different between CerS2 null and wild type mice, including well-characterized changes previously associated with this phenotype. Our results show the Q-RAI DIA as a reliable option to perform simultaneous identification and reproducible relative quantification of lipids in exploratory biological studies.
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Affiliation(s)
- Jing Kai Chang
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- SLING, Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Guoshou Teo
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yael Pewzner-Jung
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Anthony H Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Markus R Wenk
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- SLING, Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Hyungwon Choi
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Federico Torta
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- SLING, Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore.
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13
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Dey AK, Banarjee R, Boroumand M, Rutherford DV, Strassheim Q, Nyunt T, Olinger B, Basisty N. Translating Senotherapeutic Interventions into the Clinic with Emerging Proteomic Technologies. BIOLOGY 2023; 12:1301. [PMID: 37887011 PMCID: PMC10604147 DOI: 10.3390/biology12101301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023]
Abstract
Cellular senescence is a state of irreversible growth arrest with profound phenotypic changes, including the senescence-associated secretory phenotype (SASP). Senescent cell accumulation contributes to aging and many pathologies including chronic inflammation, type 2 diabetes, cancer, and neurodegeneration. Targeted removal of senescent cells in preclinical models promotes health and longevity, suggesting that the selective elimination of senescent cells is a promising therapeutic approach for mitigating a myriad of age-related pathologies in humans. However, moving senescence-targeting drugs (senotherapeutics) into the clinic will require therapeutic targets and biomarkers, fueled by an improved understanding of the complex and dynamic biology of senescent cell populations and their molecular profiles, as well as the mechanisms underlying the emergence and maintenance of senescence cells and the SASP. Advances in mass spectrometry-based proteomic technologies and workflows have the potential to address these needs. Here, we review the state of translational senescence research and how proteomic approaches have added to our knowledge of senescence biology to date. Further, we lay out a roadmap from fundamental biological discovery to the clinical translation of senotherapeutic approaches through the development and application of emerging proteomic technologies, including targeted and untargeted proteomic approaches, bottom-up and top-down methods, stability proteomics, and surfaceomics. These technologies are integral for probing the cellular composition and dynamics of senescent cells and, ultimately, the development of senotype-specific biomarkers and senotherapeutics (senolytics and senomorphics). This review aims to highlight emerging areas and applications of proteomics that will aid in exploring new senescent cell biology and the future translation of senotherapeutics.
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Affiliation(s)
| | | | | | | | | | | | | | - Nathan Basisty
- Translational Geroproteomics Unit, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; (A.K.D.); (R.B.); (M.B.); (D.V.R.); (Q.S.); (T.N.); (B.O.)
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14
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Dai Y, Ignatyeva N, Xu H, Wali R, Toischer K, Brandenburg S, Lenz C, Pronto J, Fakuade FE, Sossalla S, Zeisberg EM, Janshoff A, Kutschka I, Voigt N, Urlaub H, Rasmussen TB, Mogensen J, Lehnart SE, Hasenfuss G, Ebert A. An Alternative Mechanism of Subcellular Iron Uptake Deficiency in Cardiomyocytes. Circ Res 2023; 133:e19-e46. [PMID: 37313752 DOI: 10.1161/circresaha.122.321157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 05/26/2023] [Indexed: 06/15/2023]
Abstract
BACKGROUND Systemic defects in intestinal iron absorption, circulation, and retention cause iron deficiency in 50% of patients with heart failure. Defective subcellular iron uptake mechanisms that are independent of systemic absorption are incompletely understood. The main intracellular route for iron uptake in cardiomyocytes is clathrin-mediated endocytosis. METHODS We investigated subcellular iron uptake mechanisms in patient-derived and CRISPR/Cas-edited induced pluripotent stem cell-derived cardiomyocytes as well as patient-derived heart tissue. We used an integrated platform of DIA-MA (mass spectrometry data-independent acquisition)-based proteomics and signaling pathway interrogation. We employed a genetic induced pluripotent stem cell model of 2 inherited mutations (TnT [troponin T]-R141W and TPM1 [tropomyosin 1]-L185F) that lead to dilated cardiomyopathy (DCM), a frequent cause of heart failure, to study the underlying molecular dysfunctions of DCM mutations. RESULTS We identified a druggable molecular pathomechanism of impaired subcellular iron deficiency that is independent of systemic iron metabolism. Clathrin-mediated endocytosis defects as well as impaired endosome distribution and cargo transfer were identified as a basis for subcellular iron deficiency in DCM-induced pluripotent stem cell-derived cardiomyocytes. The clathrin-mediated endocytosis defects were also confirmed in the hearts of patients with DCM with end-stage heart failure. Correction of the TPM1-L185F mutation in DCM patient-derived induced pluripotent stem cells, treatment with a peptide, Rho activator II, or iron supplementation rescued the molecular disease pathway and recovered contractility. Phenocopying the effects of the TPM1-L185F mutation into WT induced pluripotent stem cell-derived cardiomyocytes could be ameliorated by iron supplementation. CONCLUSIONS Our findings suggest that impaired endocytosis and cargo transport resulting in subcellular iron deficiency could be a relevant pathomechanism for patients with DCM carrying inherited mutations. Insight into this molecular mechanism may contribute to the development of treatment strategies and risk management in heart failure.
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Affiliation(s)
- Yuanyuan Dai
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
| | - Nadezda Ignatyeva
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
| | - Hang Xu
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
| | - Ruheen Wali
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
| | - Karl Toischer
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Heart Center, Clinic for Cardiology and Pneumology, University Medical Center Goettingen (K.T., S.B., S.S., G.H.), University of Goettingen, Germany
| | - Sören Brandenburg
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Heart Center, Clinic for Cardiology and Pneumology, University Medical Center Goettingen (K.T., S.B., S.S., G.H.), University of Goettingen, Germany
| | - Christof Lenz
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Department of Clinical Chemistry, University Medical Center Goettingen, (C.L., H.U.), University of Goettingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC; C.L., F.E.F., N.V., S.E.L.), University of Goettingen, Germany
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Goettingen (C.L., H.U.)
| | - Julius Pronto
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen, (J.P., F.E.F., N.V.), University of Goettingen, Germany
| | - Funsho E Fakuade
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen, (J.P., F.E.F., N.V.), University of Goettingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC; C.L., F.E.F., N.V., S.E.L.), University of Goettingen, Germany
| | - Samuel Sossalla
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- Heart Center, Clinic for Cardiology and Pneumology, University Medical Center Goettingen (K.T., S.B., S.S., G.H.), University of Goettingen, Germany
- Department for Internal Medicine II, University Medical Center Regensburg (S.S.)
| | - Elisabeth M Zeisberg
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
| | - Andreas Janshoff
- Institute for Physical Chemistry (A.J.), University of Goettingen, Germany
| | - Ingo Kutschka
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Department of Thoracic and Cardiovascular Surgery, University Medical Center Göttingen (I.K.)
| | - Niels Voigt
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen, (J.P., F.E.F., N.V.), University of Goettingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC; C.L., F.E.F., N.V., S.E.L.), University of Goettingen, Germany
| | - Henning Urlaub
- Department of Clinical Chemistry, University Medical Center Goettingen, (C.L., H.U.), University of Goettingen, Germany
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Goettingen (C.L., H.U.)
| | | | - Jens Mogensen
- Department of Cardiology, Aalborg University Hospital, Denmark (J.M.)
| | - Stephan E Lehnart
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC; C.L., F.E.F., N.V., S.E.L.), University of Goettingen, Germany
| | - Gerd Hasenfuss
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Heart Center, Clinic for Cardiology and Pneumology, University Medical Center Goettingen (K.T., S.B., S.S., G.H.), University of Goettingen, Germany
| | - Antje Ebert
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
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15
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Pecori R, Ren W, Pirmoradian M, Wang X, Liu D, Berglund M, Li W, Tasakis RN, Di Giorgio S, Ye X, Li X, Arnold A, Wüst S, Schneider M, Selvasaravanan KD, Fuell Y, Stafforst T, Amini RM, Sonnevi K, Enblad G, Sander B, Wahlin BE, Wu K, Zhang H, Helm D, Binder M, Papavasiliou FN, Pan-Hammarström Q. ADAR1-mediated RNA editing promotes B cell lymphomagenesis. iScience 2023; 26:106864. [PMID: 37255666 PMCID: PMC10225930 DOI: 10.1016/j.isci.2023.106864] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 02/27/2023] [Accepted: 05/08/2023] [Indexed: 06/01/2023] Open
Abstract
Diffuse large B cell lymphoma (DLBCL) is one of the most common types of aggressive lymphoid malignancies. Here, we explore the contribution of RNA editing to DLBCL pathogenesis. We observed that DNA mutations and RNA editing events are often mutually exclusive, suggesting that tumors can modulate pathway outcomes by altering sequences at either the genomic or the transcriptomic level. RNA editing targets transcripts within known disease-driving pathways such as apoptosis, p53 and NF-κB signaling, as well as the RIG-I-like pathway. In this context, we show that ADAR1-mediated editing within MAVS transcript positively correlates with MAVS protein expression levels, associating with increased interferon/NF-κB signaling and T cell exhaustion. Finally, using targeted RNA base editing tools to restore editing within MAVS 3'UTR in ADAR1-deficient cells, we demonstrate that editing is likely to be causal to an increase in downstream signaling in the absence of activation by canonical nucleic acid receptor sensing.
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Affiliation(s)
- Riccardo Pecori
- Division of Immune Diversity (D150), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Helmholtz Institute for Translational Oncology (HI-TRON), Mainz, Germany
| | - Weicheng Ren
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Mohammad Pirmoradian
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Xianhuo Wang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Dongbing Liu
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Shenzhen, China
| | - Mattias Berglund
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Wei Li
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Rafail Nikolaos Tasakis
- Division of Immune Diversity (D150), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Graduate Program in Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Salvatore Di Giorgio
- Division of Immune Diversity (D150), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Xiaofei Ye
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Xiaobo Li
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Shenzhen, China
| | - Annette Arnold
- Division of Immune Diversity (D150), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sandra Wüst
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Schneider
- Proteomics Core Facility (W120), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Yvonne Fuell
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Thorsten Stafforst
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Rose-Marie Amini
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Kristina Sonnevi
- Hematology Unit, Department of Medicine, Huddinge, Karolinska Institutet and Medical Unit Hematology, Karolinska University Hospital, Solna, StockholmSweden
| | - Gunilla Enblad
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Birgitta Sander
- Department of Laboratory Medicine, Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Björn Engelbrekt Wahlin
- Hematology Unit, Department of Medicine, Huddinge, Karolinska Institutet and Medical Unit Hematology, Karolinska University Hospital, Solna, StockholmSweden
| | - Kui Wu
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Shenzhen, China
| | - Huilai Zhang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Dominic Helm
- Proteomics Core Facility (W120), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marco Binder
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - F. Nina Papavasiliou
- Division of Immune Diversity (D150), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Graduate Program in Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Qiang Pan-Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- BGI-Shenzhen, Shenzhen, China
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16
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Li X, Huang Y, Zheng K, Yu G, Wang Q, Gu L, Li J, Wang H, Zhang W, Sun Y, Li C. Integrated proteomic and phosphoproteomic data-independent acquisition data evaluate the personalized drug responses of primary and metastatic tumors in colorectal cancer. BIOPHYSICS REPORTS 2023; 9:67-81. [PMID: 37753059 PMCID: PMC10518519 DOI: 10.52601/bpr.2022.210048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 11/18/2022] [Indexed: 02/19/2023] Open
Abstract
Mass spectrometry (MS)-based proteomics and phosphoproteomics are powerful methods to study the biological mechanisms, diagnostic biomarkers, prognostic analysis, and drug therapy of tumors. Data-independent acquisition (DIA) mode is considered to perform better than data-dependent acquisition (DDA) mode in terms of quantitative reproducibility, specificity, accuracy, and identification of low-abundance proteins. Mini patient derived xenograft (MiniPDX) model is an effective model to assess the response to antineoplastic drugs in vivo and is helpful for the precise treatment of cancer patients. Kinases are favorable spots for tumor-targeted drugs, and their functional completion relies on signaling pathways through phosphorylating downstream substrates. Kinase-phosphorylation networks or edge interactions are considered more credible and permanent for characterizing complex diseases. Here, we provide a workflow for personalized drug response assessment in primary and metastatic colorectal cancer (CRC) tumors using DIA proteomic data, DIA phosphoproteomic data, and MiniPDX models. Three kinase inhibitors, afatinib, gefitinib, and regorafenib, are tested pharmacologically. The process mainly includes the following steps: clinical tissue collection, sample preparation, hybrid spectral libraries establishment, MS data acquisition, kinase-substrate network construction, in vivo drug test, and elastic regression modeling. Our protocol gives a more direct data basis for individual drug responses, and will improve the selection of treatment strategies for patients without the druggable mutation.
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Affiliation(s)
- Xumiao Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yiming Huang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Kuo Zheng
- Colorectal Surgery Department, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Guanyu Yu
- Colorectal Surgery Department, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Qinqin Wang
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lei Gu
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jingquan Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hui Wang
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Wei Zhang
- Colorectal Surgery Department, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Yidi Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chen Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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17
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Musiał N, Bogucka A, Tretiakow D, Skorek A, Ryl J, Czaplewska P. Proteomic analysis of sialoliths from calcified, lipid and mixed groups as a source of potential biomarkers of deposit formation in the salivary glands. Clin Proteomics 2023; 20:11. [PMID: 36949424 PMCID: PMC10035263 DOI: 10.1186/s12014-023-09402-3] [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: 01/12/2023] [Accepted: 03/08/2023] [Indexed: 03/24/2023] Open
Abstract
Salivary stones, also known as sialoliths, are formed in a pathological situation in the salivary glands. So far, neither the mechanism of their formation nor the factors predisposing to their formation are known despite several hypotheses. While they do not directly threaten human life, they significantly deteriorate the patient's quality of life. Although this is not a typical research material, attempts are made to apply various analytical tools to characterise sialoliths and search for the biomarkers in their proteomes. In this work, we used mass spectrometry and SWATH-MS qualitative and quantitative analysis to investigate the composition and select proteins that may contribute to solid deposits in the salivary glands. Twenty sialoliths, previously characterized spectroscopically and divided into the following groups: calcified (CAL), lipid (LIP) and mixed (MIX), were used for the study. Proteins unique for each of the groups were found, including: for the CAL group among them, e.g. proteins from the S100 group (S100 A8/A12 and P), mucin 7 (MUC7), keratins (KRT1/2/4/5/13), elastase (ELANE) or stomatin (STOM); proteins for the LIP group-transthyretin (TTR), lactotransferrin (LTF), matrix Gla protein (MPG), submandibular gland androgen-regulated protein 3 (SMR3A); mixed stones had the fewest unique proteins. Bacterial proteins present in sialoliths have also been identified. The analysis of the results indicates the possible role of bacterial infections, disturbances in calcium metabolism and neutrophil extracellular traps (NETs) in the formation of sialoliths.
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Affiliation(s)
- Natalia Musiał
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307, Gdańsk, Poland.
| | - Aleksandra Bogucka
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307, Gdańsk, Poland
- Institute of Biochemistry, Medical Faculty, Justus Liebig University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany
| | - Dmitry Tretiakow
- Department of Otolaryngology, Faculty of Medicine, Medical University of Gdańsk, Smoluchowskiego 17, 80-214, Gdańsk, Poland
| | - Andrzej Skorek
- Department of Otolaryngology, Faculty of Medicine, Medical University of Gdańsk, Smoluchowskiego 17, 80-214, Gdańsk, Poland
| | - Jacek Ryl
- Division of Electrochemistry and Surface Physical Chemistry, Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, G. Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - Paulina Czaplewska
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307, Gdańsk, Poland.
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18
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Schoger E, Bleckwedel F, Germena G, Rocha C, Tucholla P, Sobitov I, Möbius W, Sitte M, Lenz C, Samak M, Hinkel R, Varga ZV, Giricz Z, Salinas G, Gross JC, Zelarayán LC. Single-cell transcriptomics reveal extracellular vesicles secretion with a cardiomyocyte proteostasis signature during pathological remodeling. Commun Biol 2023; 6:79. [PMID: 36681760 PMCID: PMC9867722 DOI: 10.1038/s42003-022-04402-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 12/23/2022] [Indexed: 01/22/2023] Open
Abstract
Aberrant Wnt activation has been reported in failing cardiomyocytes. Here we present single cell transcriptome profiling of hearts with inducible cardiomyocyte-specific Wnt activation (β-catΔex3) as well as with compensatory and failing hypertrophic remodeling. We show that functional enrichment analysis points to an involvement of extracellular vesicles (EVs) related processes in hearts of β-catΔex3 mice. A proteomic analysis of in vivo cardiac derived EVs from β-catΔex3 hearts has identified differentially enriched proteins involving 20 S proteasome constitutes, protein quality control (PQC), chaperones and associated cardiac proteins including α-Crystallin B (CRYAB) and sarcomeric components. The hypertrophic model confirms that cardiomyocytes reacted with an acute early transcriptional upregulation of exosome biogenesis processes and chaperones transcripts including CRYAB, which is ameliorated in advanced remodeling. Finally, human induced pluripotent stem cells (iPSC)-derived cardiomyocytes subjected to pharmacological Wnt activation recapitulated the increased expression of exosomal markers, CRYAB accumulation and increased PQC signaling. These findings reveal that secretion of EVs with a proteostasis signature contributes to early patho-physiological adaptation of cardiomyocytes, which may serve as a read-out of disease progression and can be used for monitoring cellular remodeling in vivo with a possible diagnostic and prognostic role in the future.
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Affiliation(s)
- Eric Schoger
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen (UMG), 37075, Göttingen, Germany
- German Center for Cardiovascular Research (DZHK) partner site Göttingen, 37075, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075, Göttingen, Germany
| | - Federico Bleckwedel
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen (UMG), 37075, Göttingen, Germany
- German Center for Cardiovascular Research (DZHK) partner site Göttingen, 37075, Göttingen, Germany
| | - Giulia Germena
- German Center for Cardiovascular Research (DZHK) partner site Göttingen, 37075, Göttingen, Germany
- Laboratory Animal Science Unit, Leibnitz-Institut für Primatenforschung, Deutsches Primatenzentrum GmbH, 37075, Göttingen, Germany
| | - Cheila Rocha
- Laboratory Animal Science Unit, Leibnitz-Institut für Primatenforschung, Deutsches Primatenzentrum GmbH, 37075, Göttingen, Germany
| | - Petra Tucholla
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen (UMG), 37075, Göttingen, Germany
- German Center for Cardiovascular Research (DZHK) partner site Göttingen, 37075, Göttingen, Germany
| | - Izzatullo Sobitov
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen (UMG), 37075, Göttingen, Germany
- German Center for Cardiovascular Research (DZHK) partner site Göttingen, 37075, Göttingen, Germany
| | - Wiebke Möbius
- Max-Planck-Institute for Multidisciplinary Sciences, 37075, Göttingen, Germany
| | - Maren Sitte
- NGS Integrative Genomics Core Unit (NIG), University Medical Center Göttingen (UMG), 37075, Göttingen, Germany
| | - Christof Lenz
- Department of Clinical Chemistry, University Medical Center Göttingen (UMG), 37075, Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37075, Göttingen, Germany
| | - Mostafa Samak
- German Center for Cardiovascular Research (DZHK) partner site Göttingen, 37075, Göttingen, Germany
- Laboratory Animal Science Unit, Leibnitz-Institut für Primatenforschung, Deutsches Primatenzentrum GmbH, 37075, Göttingen, Germany
| | - Rabea Hinkel
- German Center for Cardiovascular Research (DZHK) partner site Göttingen, 37075, Göttingen, Germany
- Laboratory Animal Science Unit, Leibnitz-Institut für Primatenforschung, Deutsches Primatenzentrum GmbH, 37075, Göttingen, Germany
- Institute for Animal Hygiene, Animal Welfare and Farm Animal Behaviour (ITTN), Stiftung Tierärztliche Hochschule Hannover, University of Veterinary Medicine, 30173, Hannover, Germany
| | - Zoltán V Varga
- HCEMM-SU Cardiometabolic Immunology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, H-1085, Budapest, Hungary
- Pharmahungary Group, H-1085, Budapest, Hungary
| | - Zoltán Giricz
- HCEMM-SU Cardiometabolic Immunology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, H-1085, Budapest, Hungary
- Pharmahungary Group, H-1085, Budapest, Hungary
| | - Gabriela Salinas
- NGS Integrative Genomics Core Unit (NIG), University Medical Center Göttingen (UMG), 37075, Göttingen, Germany
| | - Julia C Gross
- Health and Medical University, D-14471, Potsdam, Germany
| | - Laura C Zelarayán
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen (UMG), 37075, Göttingen, Germany.
- German Center for Cardiovascular Research (DZHK) partner site Göttingen, 37075, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075, Göttingen, Germany.
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19
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Kellie JF, Schneck NA, Causon JC, Baba T, Mehl JT, Pohl KI. Top-Down Characterization and Intact Mass Quantitation of a Monoclonal Antibody Drug from Serum by Use of a Quadrupole TOF MS System Equipped with Electron-Activated Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:17-26. [PMID: 36459688 DOI: 10.1021/jasms.2c00206] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Time-of-flight MS systems for biopharmaceutical and protein characterization applications may play an even more pivotal role in the future as biotherapeutics increase in drug pipelines and as top-down MS approaches increase in use. Here, a recently developed TOF MS system is examined for monoclonal antibody (mAb) characterization from serum samples. After immunocapture, purified drug material spiked into monkey serum or dosed for an in-life study is analyzed by top-down MS. While characterization aspects are a distinct advantage of the MS platform, MS system and software capabilities are also shown regarding intact protein quantitation. Such applications are demonstrated to help enable comprehensive protein molecule quantitation and characterization by use of TOF MS instrumentation.
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Affiliation(s)
- John F Kellie
- GSK, Collegeville, Pennsylvania 19426, United States
| | | | | | | | - John T Mehl
- GSK, Collegeville, Pennsylvania 19426, United States
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20
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Ahmed EA, El-Derany MO, Anwar AM, Saied EM, Magdeldin S. Metabolomics and Lipidomics Screening Reveal Reprogrammed Signaling Pathways toward Cancer Development in Non-Alcoholic Steatohepatitis. Int J Mol Sci 2022; 24:ijms24010210. [PMID: 36613653 PMCID: PMC9820351 DOI: 10.3390/ijms24010210] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/09/2022] [Accepted: 11/19/2022] [Indexed: 12/24/2022] Open
Abstract
With the rising incidence of hepatocellular carcinoma (HCC) from non-alcoholic steatohepatitis (NASH), identifying new metabolic readouts that function in metabolic pathway perpetuation is still a demand. The study aimed to compare the metabolic signature between NASH and NASH-HCC patients to explore novel reprogrammed metabolic pathways that might modulate cancer progression in NASH patients. NASH and NASH-HCC patients were recruited and screened for metabolomics, and isotope-labeled lipidomics were targeted and profiled using the EXION-LCTM system equipped with a Triple-TOFTM 5600+ system. Results demonstrated significantly (p ≤ 0.05) higher levels of triacylglycerol, AFP, AST, and cancer antigen 19-9 in NASH-HCC than in NASH patients, while prothrombin time, platelet count, and total leukocyte count were decreased significantly (p ≤ 0.05). Serum metabolic profiling showed a panel of twenty metabolites with 10% FDR and p ≤ 0.05 in both targeted and non-targeted analysis that could segregate NASH-HCC from NASH patients. Pathway analysis revealed that the metabolites are implicated in the down-regulation of necroptosis, amino acid metabolism, and regulation of lipid metabolism by PPAR-α, biogenic amine synthesis, fatty acid metabolism, and the mTOR signaling pathway. Cholesterol metabolism, DNA repair, methylation pathway, bile acid, and salts metabolism were significantly upregulated in NASH-HCC compared to the NASH group. Metabolite-protein interactions network analysis clarified a set of well-known protein encoding genes that play crucial roles in cancer, including PEMT, IL4I1, BAAT, TAT, CDKAL1, NNMT, PNP, NOS1, and AHCYL. Taken together, reliable metabolite fingerprints are presented and illustrated in a detailed map for the most predominant reprogrammed metabolic pathways that target HCC development from NASH.
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Affiliation(s)
- Eman A. Ahmed
- Proteomics and Metabolomics Research Program, Department of Basic Research, Children’s Cancer Hospital 57357, Cairo 11441, Egypt
- Department of Pharmacology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Marwa O. El-Derany
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Ali Mostafa Anwar
- Proteomics and Metabolomics Research Program, Department of Basic Research, Children’s Cancer Hospital 57357, Cairo 11441, Egypt
| | - Essa M. Saied
- Chemistry Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
- Institute for Chemistry, Humboldt Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - Sameh Magdeldin
- Proteomics and Metabolomics Research Program, Department of Basic Research, Children’s Cancer Hospital 57357, Cairo 11441, Egypt
- Department of Physiology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
- Correspondence: ; Tel.: +20-(10)-64962210
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21
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Andreyeva EN, Emelyanov AV, Nevil M, Sun L, Vershilova E, Hill CA, Keogh MC, Duronio RJ, Skoultchi AI, Fyodorov DV. Drosophila SUMM4 complex couples insulator function and DNA replication control. eLife 2022; 11:e81828. [PMID: 36458689 PMCID: PMC9917439 DOI: 10.7554/elife.81828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
Asynchronous replication of chromosome domains during S phase is essential for eukaryotic genome function, but the mechanisms establishing which domains replicate early versus late in different cell types remain incompletely understood. Intercalary heterochromatin domains replicate very late in both diploid chromosomes of dividing cells and in endoreplicating polytene chromosomes where they are also underreplicated. Drosophila SNF2-related factor SUUR imparts locus-specific underreplication of polytene chromosomes. SUUR negatively regulates DNA replication fork progression; however, its mechanism of action remains obscure. Here, we developed a novel method termed MS-Enabled Rapid protein Complex Identification (MERCI) to isolate a stable stoichiometric native complex SUMM4 that comprises SUUR and a chromatin boundary protein Mod(Mdg4)-67.2. Mod(Mdg4) stimulates SUUR ATPase activity and is required for a normal spatiotemporal distribution of SUUR in vivo. SUUR and Mod(Mdg4)-67.2 together mediate the activities of gypsy insulator that prevent certain enhancer-promoter interactions and establish euchromatin-heterochromatin barriers in the genome. Furthermore, SuUR or mod(mdg4) mutations reverse underreplication of intercalary heterochromatin. Thus, SUMM4 can impart late replication of intercalary heterochromatin by attenuating the progression of replication forks through euchromatin/heterochromatin boundaries. Our findings implicate a SNF2 family ATP-dependent motor protein SUUR in the insulator function, reveal that DNA replication can be delayed by a chromatin barrier, and uncover a critical role for architectural proteins in replication control. They suggest a mechanism for the establishment of late replication that does not depend on an asynchronous firing of late replication origins.
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Affiliation(s)
- Evgeniya N Andreyeva
- Department of Cell Biology, Albert Einstein College of MedicineBronxUnited States
| | | | - Markus Nevil
- UNC-SPIRE, University of North CarolinaChapel HillUnited States
| | - Lu Sun
- EpiCypherDurhamUnited States
| | - Elena Vershilova
- Department of Cell Biology, Albert Einstein College of MedicineBronxUnited States
| | - Christina A Hill
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel HillChapel HillUnited States
| | | | - Robert J Duronio
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel HillChapel HillUnited States
- Lineberger Comprehensive Cancer Center, University of North CarolinaChapel HillUnited States
- Department of Biology, University of North CarolinaChapel HillUnited States
- Department of Genetics, University of North CarolinaChapel HillUnited States
| | - Arthur I Skoultchi
- Department of Cell Biology, Albert Einstein College of MedicineBronxUnited States
| | - Dmitry V Fyodorov
- Department of Cell Biology, Albert Einstein College of MedicineBronxUnited States
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22
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Yang Y, Liang S, Geng H, Xiong M, Li M, Su Q, Jia F, Zhao Y, Wang K, Jiang J, Qin S, Li X. Proteomics revealed the crosstalk between copper stress and cuproptosis, and explored the feasibility of curcumin as anticancer copper ionophore. Free Radic Biol Med 2022; 193:638-647. [PMID: 36395954 DOI: 10.1016/j.freeradbiomed.2022.11.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/11/2022] [Accepted: 11/13/2022] [Indexed: 11/16/2022]
Abstract
As an essential micronutrient element in organisms, copper controls a host of fundamental cellular functions. Recently, copper-dependent cell growth and proliferation have been defined as "cuproplasia". Conversely, "cuproptosis" represents copper-dependent cell death, in a nonapoptotic manner. So far, a series of copper ionophores have been developed to kill cancer cells. However, the biological response mechanism of copper uptake has not been systematically analyzed. Based on quantitative proteomics, we revealed the crosstalk between copper stress and cuproptosis in cancer cells, and also explored the feasibility of curcumin as anticancer copper ionophore. Copper stress not only couples with cuproptosis, but also leads to reactive oxygen species (ROS) stress, oxidative damage and cell cycle arrest. In cancer cells, a feedback cytoprotection mechanism involving cuproptosis mediators was discovered. During copper treatment, the activation of glutamine transporters and the loss of Fe-S cluster proteins are the facilitators and results of cuproptosis, respectively. Through copper depletion, glutathione (GSH) blocks the cuproptosis process, rescues the activation of glutamine transporters, and prevents the loss of Fe-S cluster proteins, except for protecting cancer cells from apoptosis, protein degradation and oxidative damage. In addition, the copper ionophore curcumin can control the metabolisms of lipids, RNA, NADH and NADPH in colorectal cancer cells, and also up-regulates positive cuproptosis mediators. This work not only established the crosstalk between copper stress and cuproptosis, but also discolored the suppression and acceleration of cuproptosis by GSH and curcumin, respectively. Our results are significant for understanding cuproptosis process and developing novel anticancer reagents based on cuproptosis.
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Affiliation(s)
- Ying Yang
- College of Health Science and Engineering, Hubei University, Wuhan, 430062, Hubei, PR China; Hubei Province Engineering Center of Performance Chemicals, Hubei University, Wuhan, 430062, Hubei, PR China
| | - Shuyu Liang
- College of Chemistry and Molecular Engineering, Peking University, 100871, Beijing, PR China
| | - Hongen Geng
- School of Chemistry, Central China Normal University, Wuhan, 430079, Hubei, PR China
| | - Mengmeng Xiong
- College of Health Science and Engineering, Hubei University, Wuhan, 430062, Hubei, PR China; Hubei Province Engineering Center of Performance Chemicals, Hubei University, Wuhan, 430062, Hubei, PR China
| | - Man Li
- School of Chemistry, Central China Normal University, Wuhan, 430079, Hubei, PR China
| | - Qian Su
- Department of Endocrinology, The Third Affiliated Hospital of Chongqing Medical University, 401120, Chongqing, PR China
| | - Fang Jia
- College of Health Science and Engineering, Hubei University, Wuhan, 430062, Hubei, PR China; Hubei Province Engineering Center of Performance Chemicals, Hubei University, Wuhan, 430062, Hubei, PR China
| | - Yimei Zhao
- College of Health Science and Engineering, Hubei University, Wuhan, 430062, Hubei, PR China.
| | - Kai Wang
- College of Health Science and Engineering, Hubei University, Wuhan, 430062, Hubei, PR China; Hubei Province Engineering Center of Performance Chemicals, Hubei University, Wuhan, 430062, Hubei, PR China
| | - Jun Jiang
- College of Health Science and Engineering, Hubei University, Wuhan, 430062, Hubei, PR China; Hubei Province Engineering Center of Performance Chemicals, Hubei University, Wuhan, 430062, Hubei, PR China
| | - Si Qin
- Department of Endocrinology, The Third Affiliated Hospital of Chongqing Medical University, 401120, Chongqing, PR China.
| | - Xiang Li
- College of Health Science and Engineering, Hubei University, Wuhan, 430062, Hubei, PR China; Hubei Province Engineering Center of Performance Chemicals, Hubei University, Wuhan, 430062, Hubei, PR China.
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23
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Metabolic profiling workflow for cell extracts by targeted hydrophilic interaction liquid chromatography-tandem mass spectrometry. J Chromatogr A 2022; 1684:463556. [DOI: 10.1016/j.chroma.2022.463556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/22/2022]
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24
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Stejerean‐Todoran I, Zimmermann K, Gibhardt CS, Vultur A, Ickes C, Shannan B, Bonilla del Rio Z, Wölling A, Cappello S, Sung H, Shumanska M, Zhang X, Nanadikar M, Latif MU, Wittek A, Lange F, Waters A, Brafford P, Wilting J, Urlaub H, Katschinski DM, Rehling P, Lenz C, Jakobs S, Ellenrieder V, Roesch A, Schön MP, Herlyn M, Stanisz H, Bogeski I. MCU
controls melanoma progression through a redox‐controlled phenotype switch. EMBO Rep 2022; 23:e54746. [PMID: 36156348 PMCID: PMC9638851 DOI: 10.15252/embr.202254746] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 08/29/2022] [Accepted: 08/29/2022] [Indexed: 01/16/2023] Open
Abstract
Melanoma is the deadliest of skin cancers and has a high tendency to metastasize to distant organs. Calcium and metabolic signals contribute to melanoma invasiveness; however, the underlying molecular details are elusive. The MCU complex is a major route for calcium into the mitochondrial matrix but whether MCU affects melanoma pathobiology was not understood. Here, we show that MCUA expression correlates with melanoma patient survival and is decreased in BRAF kinase inhibitor‐resistant melanomas. Knockdown (KD) of MCUA suppresses melanoma cell growth and stimulates migration and invasion. In melanoma xenografts, MCUA_KD reduces tumor volumes but promotes lung metastases. Proteomic analyses and protein microarrays identify pathways that link MCUA and melanoma cell phenotype and suggest a major role for redox regulation. Antioxidants enhance melanoma cell migration, while prooxidants diminish the MCUA_KD‐induced invasive phenotype. Furthermore, MCUA_KD increases melanoma cell resistance to immunotherapies and ferroptosis. Collectively, we demonstrate that MCUA controls melanoma aggressive behavior and therapeutic sensitivity. Manipulations of mitochondrial calcium and redox homeostasis, in combination with current therapies, should be considered in treating advanced melanoma.
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Affiliation(s)
- Ioana Stejerean‐Todoran
- Molecular Physiology, Department of Cardiovascular Physiology, University Medical Center Georg‐August‐University Göttingen Germany
| | | | - Christine S Gibhardt
- Molecular Physiology, Department of Cardiovascular Physiology, University Medical Center Georg‐August‐University Göttingen Germany
| | - Adina Vultur
- Molecular Physiology, Department of Cardiovascular Physiology, University Medical Center Georg‐August‐University Göttingen Germany
- The Wistar Institute Melanoma Research Center Philadelphia PA USA
| | - Christian Ickes
- Molecular Physiology, Department of Cardiovascular Physiology, University Medical Center Georg‐August‐University Göttingen Germany
| | - Batool Shannan
- The Wistar Institute Melanoma Research Center Philadelphia PA USA
- Department of Dermatology, University Hospital Essen, West German Cancer Center University Duisburg‐Essen and the German Cancer Consortium (DKTK)
| | - Zuriñe Bonilla del Rio
- Molecular Physiology, Department of Cardiovascular Physiology, University Medical Center Georg‐August‐University Göttingen Germany
| | - Anna Wölling
- Department of Dermatology, Venereology and Allergology, University Medical Center Georg‐August‐University Göttingen Germany
| | - Sabrina Cappello
- Molecular Physiology, Department of Cardiovascular Physiology, University Medical Center Georg‐August‐University Göttingen Germany
| | - Hsu‐Min Sung
- Molecular Physiology, Department of Cardiovascular Physiology, University Medical Center Georg‐August‐University Göttingen Germany
| | - Magdalena Shumanska
- Molecular Physiology, Department of Cardiovascular Physiology, University Medical Center Georg‐August‐University Göttingen Germany
| | - Xin Zhang
- Molecular Physiology, Department of Cardiovascular Physiology, University Medical Center Georg‐August‐University Göttingen Germany
| | - Maithily Nanadikar
- Department of Cardiovascular Physiology, University Medical Center Göttingen Georg‐August‐University Göttingen Germany
| | - Muhammad U Latif
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology University Medical Center Göttingen Gottingen Germany
| | - Anna Wittek
- Department of NanoBiophotonics Max Planck Institute for Multidisciplinary Sciences Göttingen Germany
- Clinic of Neurology University Medical Center Göttingen Göttingen Germany
| | - Felix Lange
- Department of NanoBiophotonics Max Planck Institute for Multidisciplinary Sciences Göttingen Germany
- Clinic of Neurology University Medical Center Göttingen Göttingen Germany
| | - Andrea Waters
- The Wistar Institute Melanoma Research Center Philadelphia PA USA
| | | | - Jörg Wilting
- Department of Anatomy and Cell Biology, University Medical Center Georg‐August‐University Göttingen Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group Max Planck Institute for Multidisciplinary Sciences Göttingen Germany
- Bioanalytics, Institute of Clinical Chemistry University Medical Center Göttingen Germany
| | - Dörthe M Katschinski
- Department of Cardiovascular Physiology, University Medical Center Göttingen Georg‐August‐University Göttingen Germany
| | - Peter Rehling
- Department of Cellular Biochemistry University Medical Center Göttingen, GZMB Göttingen Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry Group Max Planck Institute for Multidisciplinary Sciences Göttingen Germany
- Bioanalytics, Institute of Clinical Chemistry University Medical Center Göttingen Germany
| | - Stefan Jakobs
- Department of NanoBiophotonics Max Planck Institute for Multidisciplinary Sciences Göttingen Germany
- Clinic of Neurology University Medical Center Göttingen Göttingen Germany
| | - Volker Ellenrieder
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology University Medical Center Göttingen Gottingen Germany
| | - Alexander Roesch
- Department of Dermatology, University Hospital Essen, West German Cancer Center University Duisburg‐Essen and the German Cancer Consortium (DKTK)
| | - Michael P Schön
- Department of Dermatology, Venereology and Allergology, University Medical Center Georg‐August‐University Göttingen Germany
| | - Meenhard Herlyn
- The Wistar Institute Melanoma Research Center Philadelphia PA USA
| | - Hedwig Stanisz
- Department of Dermatology, Venereology and Allergology, University Medical Center Georg‐August‐University Göttingen Germany
| | - Ivan Bogeski
- Molecular Physiology, Department of Cardiovascular Physiology, University Medical Center Georg‐August‐University Göttingen Germany
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A Novel Approach of SWATH-Based Metabolomics Analysis Using the Human Metabolome Database Spectral Library. Int J Mol Sci 2022; 23:ijms231810908. [PMID: 36142821 PMCID: PMC9500730 DOI: 10.3390/ijms231810908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/04/2022] [Accepted: 09/07/2022] [Indexed: 11/22/2022] Open
Abstract
Metabolomics is a potential approach to paving new avenues for clinical diagnosis, molecular medicine, and therapeutic drug monitoring and development. The conventional metabolomics analysis pipeline depends on the data-independent acquisition (DIA) technique. Although powerful, it still suffers from stochastic, non-reproducible ion selection across samples. Despite the presence of different metabolomics workbenches, metabolite identification remains a tedious and time-consuming task. Consequently, sequential windowed acquisition of all theoretical MS (SWATH) acquisition has attracted much attention to overcome this limitation. This article aims to develop a novel SWATH platform for data analysis with a generation of an accurate mass spectral library for metabolite identification using SWATH acquisition. The workflow was validated using inclusion/exclusion compound lists. The false-positive identification was 3.4% from the non-endogenous drugs with 96.6% specificity. The workflow has proven to overcome background noise despite the complexity of the SWATH sample. From the Human Metabolome Database (HMDB), 1282 compounds were tested in various biological samples to demonstrate the feasibility of the workflow. The current study identified 377 compounds in positive and 303 in negative modes with 392 unique non-redundant metabolites. Finally, a free software tool, SASA, was developed to analyze SWATH-acquired samples using the proposed pipeline.
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26
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Wood SA, Hains PG, Muller A, Hill M, Premarathne S, Murtaza M, Robinson PJ, Mellick GD, Sykes AM. Proteomic profiling of idiopathic Parkinson's disease primary patient cells by SWATH-MS. Proteomics Clin Appl 2022; 16:e2200015. [PMID: 35579911 PMCID: PMC9787017 DOI: 10.1002/prca.202200015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/12/2022] [Accepted: 05/13/2022] [Indexed: 12/30/2022]
Abstract
PURPOSE Parkinson's disease (PD) is the second most prevalent neurodegenerative disease. It is generally diagnosed clinically after the irreversible loss of dopaminergic neurons and no general biomarkers currently exist. To gain insight into the underlying cellular causes of PD we aimed to quantify the proteomic differences between healthy control and PD patient cells. EXPERIMENTAL DESIGN Sequential Window Acquisition of all THeoretical Mass Spectra was performed on primary cells from healthy controls and PD patients. RESULTS In total, 1948 proteins were quantified and 228 proteins were significantly differentially expressed in PD patient cells. In PD patient cells, we identified seven significantly increased proteins involved in the unfolded protein response (UPR) and focused on cells with high and low amounts of PDIA6 and HYOU1. We discovered that PD patients with high amounts of PDIA6 and HYOU1 proteins were more sensitive to endoplasmic reticulum stress, in particular to tunicamycin. Data is available via ProteomeXchange with identifier PXD030723. CONCLUSIONS AND CLINICAL RELEVANCE This data from primary patient cells has uncovered a critical role of the UPR in patients with PD and may provide insight to the underlying cellular dysfunctions in these patients.
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Affiliation(s)
- Stephen A. Wood
- Griffith Institute for Drug DiscoveryGriffith UniversityNathanQueenslandAustralia
| | - Peter G. Hains
- Cell Signalling UnitChildren's Medical Research InstituteThe University of SydneyWestmeadNSWAustralia
| | | | - Melissa Hill
- Griffith Institute for Drug DiscoveryGriffith UniversityNathanQueenslandAustralia
| | - Susitha Premarathne
- Griffith Institute for Drug DiscoveryGriffith UniversityNathanQueenslandAustralia
| | - Mariyam Murtaza
- Griffith Institute for Drug DiscoveryGriffith UniversityNathanQueenslandAustralia
| | - Phillip J. Robinson
- Cell Signalling UnitChildren's Medical Research InstituteThe University of SydneyWestmeadNSWAustralia
| | - George D. Mellick
- Griffith Institute for Drug DiscoveryGriffith UniversityNathanQueenslandAustralia
| | - Alex M. Sykes
- Griffith Institute for Drug DiscoveryGriffith UniversityNathanQueenslandAustralia
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Linnemannstöns K, Karuna M P, Witte L, Choezom D, Honemann‐Capito M, Lagurin AS, Schmidt CV, Shrikhande S, Steinmetz L, Wiebke M, Lenz C, Gross JC. Microscopic and biochemical monitoring of endosomal trafficking and extracellular vesicle secretion in an endogenous in vivo model. J Extracell Vesicles 2022; 11:e12263. [PMID: 36103151 PMCID: PMC9473323 DOI: 10.1002/jev2.12263] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/17/2022] [Accepted: 05/22/2022] [Indexed: 11/10/2022] Open
Abstract
Extracellular vesicle (EV) secretion enables cell-cell communication in multicellular organisms. During development, EV secretion and the specific loading of signalling factors in EVs contributes to organ development and tissue differentiation. Here, we present an in vivo model to study EV secretion using the fat body and the haemolymph of the fruit fly, Drosophila melanogaster. The system makes use of tissue-specific EV labelling and is amenable to genetic modification by RNAi. This allows the unique combination of microscopic visualisation of EVs in different organs and quantitative biochemical purification to study how EVs are generated within the cells and which factors regulate their secretion in vivo. Characterisation of the system revealed that secretion of EVs from the fat body is mainly regulated by Rab11 and Rab35, highlighting the importance of recycling Rab GTPase family members for EV secretion. We furthermore discovered a so far unknown function of Rab14 along with the kinesin Klp98A in EV biogenesis and secretion.
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Affiliation(s)
- Karen Linnemannstöns
- Developmental BiochemistryUniversity Medical Center GoettingenGoettingenGermany
- Hematology and OncologyUniversity Medical Center GoettingenGoettingenGermany
- Molecular OncologyUniversity Medical Center GoettingenGoettingenGermany
| | - Pradhipa Karuna M
- Developmental BiochemistryUniversity Medical Center GoettingenGoettingenGermany
| | - Leonie Witte
- Developmental BiochemistryUniversity Medical Center GoettingenGoettingenGermany
| | - Dolma Choezom
- Developmental BiochemistryUniversity Medical Center GoettingenGoettingenGermany
| | | | - Alex Simon Lagurin
- Developmental BiochemistryUniversity Medical Center GoettingenGoettingenGermany
| | | | - Shreya Shrikhande
- Developmental BiochemistryUniversity Medical Center GoettingenGoettingenGermany
| | | | - Möbius Wiebke
- Electron Microscopy Core Unit, Department of NeurogeneticsMax Planck Institute of Experimental MedicineGöttingenGermany
| | - Christof Lenz
- Institute of Clinical ChemistryUniversity Medical Center GöttingenGöttingenGermany
- Bioanalytical Mass Spectrometry GroupMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Julia Christina Gross
- Developmental BiochemistryUniversity Medical Center GoettingenGoettingenGermany
- Hematology and OncologyUniversity Medical Center GoettingenGoettingenGermany
- Department of MedicineHealth and Medical UniversityPotsdamGermany
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28
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Impact of Clarified Apple Juices with Different Processing Methods on Gut Microbiota and Metabolomics of Rats. Nutrients 2022; 14:nu14173488. [PMID: 36079746 PMCID: PMC9460580 DOI: 10.3390/nu14173488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/09/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022] Open
Abstract
The consumption of processed foods has increased compared to that of fresh foods in recent years, especially due to the coronavirus disease 2019 pandemic. Here, we evaluated the health effects of clarified apple juices (CAJs, devoid of pectin and additives) processed to different degrees, including not-from-concentrate (NFC) and from-concentrate (FC) CAJs. A 56-day experiment including a juice-switch after 28 days was designed. An integrated analysis of 16S rRNA sequencing and untargeted metabolomics of cecal content were performed. In addition, differences in the CAJs tested with respect to nutritional indices and composition of small-molecule compounds were analyzed. The NFC CAJ, which showed a higher phenolic content resulting from the lower processing degree, could improve microbiota diversity and influence its structure. It also reduced bile acid and bilirubin contents, as well as inhibited the microbial metabolism of tryptophan in the gut. However, we found that these effects diminished with time by performing experiment extension and undertaking juice-switching. Our study provides evidence regarding the health effects of processed foods that can potentially be applied to public health policy decision making. We believe that NFC juices with a lower processing degree could potentially be healthier than FC juice.
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29
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Mendes ML, Dittmar G. Targeted proteomics on its way to discovery. Proteomics 2022; 22:e2100330. [PMID: 35816345 DOI: 10.1002/pmic.202100330] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/20/2022] [Accepted: 06/27/2022] [Indexed: 11/06/2022]
Abstract
For a long time, targeted and discovery proteomics covered different corners of the detection spectrum, with targeted proteomics focused on small target sets. This changed with the recent advances in highly multiplexed analysis. While discovery proteomics still pushes higher numbers of identified and quantified proteins, the advances in targeted proteomics rose to cover large parts of less complex proteomes or proteomes with low protein detection counts due to dynamic range restrictions, like the blood proteome. These new developments will impact, especially on the field of biomarker discovery and the possibility of using targeted proteomics for diagnostic purposes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Marta L Mendes
- Proteomics of cellular signalling, Department of Infection and Immunity, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg
| | - Gunnar Dittmar
- Proteomics of cellular signalling, Department of Infection and Immunity, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg.,Department of Life Sciences and Medicine, University of Luxembourg, L-4367, Belvaux, Luxembourg
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30
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Przepiora T, Figaj D, Bogucka A, Fikowicz-Krosko J, Czajkowski R, Hugouvieux-Cotte-Pattat N, Skorko-Glonek J. The Periplasmic Oxidoreductase DsbA Is Required for Virulence of the Phytopathogen Dickeya solani. Int J Mol Sci 2022; 23:ijms23020697. [PMID: 35054882 PMCID: PMC8775594 DOI: 10.3390/ijms23020697] [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: 11/26/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 02/01/2023] Open
Abstract
In bacteria, the DsbA oxidoreductase is a crucial factor responsible for the introduction of disulfide bonds to extracytoplasmic proteins, which include important virulence factors. A lack of proper disulfide bonds frequently leads to instability and/or loss of protein function; therefore, improper disulfide bonding may lead to avirulent phenotypes. The importance of the DsbA function in phytopathogens has not been extensively studied yet. Dickeya solani is a bacterium from the Soft Rot Pectobacteriaceae family which is responsible for very high economic losses mainly in potato. In this work, we constructed a D. solani dsbA mutant and demonstrated that a lack of DsbA caused a loss of virulence. The mutant bacteria showed lower activities of secreted virulence determinants and were unable to develop disease symptoms in a potato plant. The SWATH-MS-based proteomic analysis revealed that the dsbA mutation led to multifaceted effects in the D. solani cells, including not only lower levels of secreted virulence factors, but also the induction of stress responses. Finally, the outer membrane barrier seemed to be disturbed by the mutation. Our results clearly demonstrate that the function played by the DsbA oxidoreductase is crucial for D. solani virulence, and a lack of DsbA significantly disturbs cellular physiology.
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Affiliation(s)
- Tomasz Przepiora
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (T.P.); (D.F.)
| | - Donata Figaj
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (T.P.); (D.F.)
| | - Aleksandra Bogucka
- Laboratory of Mass Spectrometry, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-807 Gdansk, Poland;
| | - Jakub Fikowicz-Krosko
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-807 Gdansk, Poland; (J.F.-K.); (R.C.)
| | - Robert Czajkowski
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-807 Gdansk, Poland; (J.F.-K.); (R.C.)
| | - Nicole Hugouvieux-Cotte-Pattat
- Microbiologie Adaptation et Pathogénie, Université Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, Campus LyonTech-la Doua Bâtiment André Lwoff 10 rue Raphaël Dubois 69622, F69622 Villeurbanne, France;
| | - Joanna Skorko-Glonek
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (T.P.); (D.F.)
- Correspondence:
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Three Microbial Musketeers of the Seas: Shewanella baltica, Aliivibrio fischeri and Vibrio harveyi, and Their Adaptation to Different Salinity Probed by a Proteomic Approach. Int J Mol Sci 2022; 23:ijms23020619. [PMID: 35054801 PMCID: PMC8775919 DOI: 10.3390/ijms23020619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/01/2022] [Accepted: 01/04/2022] [Indexed: 11/17/2022] Open
Abstract
Osmotic changes are common challenges for marine microorganisms. Bacteria have developed numerous ways of dealing with this stress, including reprogramming of global cellular processes. However, specific molecular adaptation mechanisms to osmotic stress have mainly been investigated in terrestrial model bacteria. In this work, we aimed to elucidate the basis of adjustment to prolonged salinity challenges at the proteome level in marine bacteria. The objects of our studies were three representatives of bacteria inhabiting various marine environments, Shewanella baltica, Vibrio harveyi and Aliivibrio fischeri. The proteomic studies were performed with bacteria cultivated in increased and decreased salinity, followed by proteolytic digestion of samples which were then subjected to liquid chromatography with tandem mass spectrometry analysis. We show that bacteria adjust at all levels of their biological processes, from DNA topology through gene expression regulation and proteasome assembly, to transport and cellular metabolism. The finding that many similar adaptation strategies were observed for both low- and high-salinity conditions is particularly striking. The results show that adaptation to salinity challenge involves the accumulation of DNA-binding proteins and increased polyamine uptake. We hypothesize that their function is to coat and protect the nucleoid to counteract adverse changes in DNA topology due to ionic shifts.
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32
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Sosnowski P, Marin V, Tian X, Hopfgartner G. Analysis of illicit pills and drugs of abuse in urine samples using a 3D-printed open port probe hyphenated with differential mobility spectrometry-mass spectrometry. Analyst 2022; 147:4318-4325. [PMID: 36040388 DOI: 10.1039/d2an00925k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The present work describes the application of an in-house developed 3D-printed open port probe (3DP-OPP) with differential ion mobility spectrometry (DMS) mass spectrometry.
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Affiliation(s)
- Piotr Sosnowski
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, Quai Ernest Ansermet 24, 1211, Geneva, Switzerland
| | - Victor Marin
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, Quai Ernest Ansermet 24, 1211, Geneva, Switzerland
| | - Xiaobo Tian
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, Quai Ernest Ansermet 24, 1211, Geneva, Switzerland
| | - Gérard Hopfgartner
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, Quai Ernest Ansermet 24, 1211, Geneva, Switzerland
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Data-Independent Acquisition Mass Spectrometry-Based Deep Proteome Analysis for Hydrophobic Proteins from Dried Blood Spots Enriched by Sodium Carbonate Precipitation. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2420:39-52. [PMID: 34905164 DOI: 10.1007/978-1-0716-1936-0_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Dried blood spots (DBS) are widely used for screening molecular profiles, including enzymatic activity. However, hydrophilic proteins present in large amounts in blood inhibit detection of other proteins in DBS by liquid chromatography-mass spectrometry (LC-MS/MS) without preenrichment. Sodium carbonate precipitation (SCP) can concentrate hydrophobic proteins from DBS and effectively remove soluble hydrophilic proteins. Furthermore, SCP combination with data-independent acquisition (DIA) for quantitative LC-MS/MS enhanced the proteome analysis sensitivity and quantification limits. In this protocol, we have described in detail a simple preenrichment method using SCP and a deep proteome analysis method for LC-MS/MS data using DIA.
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34
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Chien HJ, Huang YH, Zheng YF, Wang WC, Kuo CY, Wei GJ, Lai CC. Proteomics for species authentication of cod and corresponding fishery products. Food Chem 2021; 374:131631. [PMID: 34838403 DOI: 10.1016/j.foodchem.2021.131631] [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: 01/08/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 11/27/2022]
Abstract
Seafood substitutions is a global problem and come under the spotlight in recent years. In Taiwan, Greenland halibut is usually substituted for the cod because of its lower price. Nowadays, DNA technology is widely used for fish species identifications; however, it still has concern about the DNA of processed fishery products might be destroyed. This study was designed to develop a proteomic-based method for fish and fishery product authentication by using ultra performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS/MS) with Sequential window acquisition of all theoretical fragment ion spectra (SWATH). The protein biomarkers from the meat of Alaska pollock, Atlantic cod, and Greenland halibut were identified and validated for species authentication of cod and corresponding fishery products, which might prevent consumer substitutions and fish product mislabeling. Besides, the E. coli proteins can be measured from existing SWATH-MS data though retrospective analysis successfully, it might present the quality of fish meat.
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Affiliation(s)
- Han-Ju Chien
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan.
| | - Yu-Han Huang
- Institute of Food Safety and Health Risk Assessment, National Yang-Ming University, Taipei 11221, Taiwan.
| | - Yi-Feng Zheng
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan.
| | - Wei-Chen Wang
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan.
| | - Cheng-Yu Kuo
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan.
| | - Guor-Jien Wei
- Institute of Food Safety and Health Risk Assessment, National Yang-Ming University, Taipei 11221, Taiwan; Metabolomics-Proteomics Research Center, National Yang-Ming University, Taipei 11221, Taiwan.
| | - Chien-Chen Lai
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan; Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan; Graduate Institute of Chinese Medical Science, China Medical University, Taichung 40402, Taiwan.
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35
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N Diaye K, Debong M, Behr J, Dirndorfer S, Duggan T, Beusch A, Schlagbauer V, Dawid C, Loos HM, Buettner A, Lang R, Hofmann T. Dietary Piperine is Transferred into the Milk of Nursing Mothers. Mol Nutr Food Res 2021; 65:e2100508. [PMID: 34633734 DOI: 10.1002/mnfr.202100508] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 09/08/2021] [Indexed: 11/11/2022]
Abstract
INTRODUCTION The diet of breastfeeding mothers could bring nurslings into contact with flavor compounds putatively contributing to early sensory programming of the infant. The study investigates whether tastants from a customary curry dish consumed by mothers are detectable in their milk afterwards and can be perceived by the infant. METHODS AND RESULTS Sensory evaluation identifies pungency as the dominating taste impression of the curry dish. Its ingredients of chili, pepper, and ginger suggest the flavor compounds capsaicin, piperine, and 6-gingerol as analytical targets. Breastfeeding mothers are recruited for an intervention trial involving the consumption of the curry dish and subsequent collection of milk samples for flavor compound analysis. Targeted and untargeted mass spectrometric (MS)- investigations identify exclusively piperine as an intervention-derived compound in human milk. However, concentrations are below the human taste threshold. CONCLUSION Piperine from pepper-containing foods transfers into the mother's milk within 1 h and is delivered to the nursling. Concentrations of 50 and 200 nM of piperine are 70-350 times below the human taste threshold, but TRPV1 (Transient Receptor Potential Vanilloid-1 ion channel) desensitization through frequent exposure to sub-taste-threshold concentrations could contribute to an increased tolerance at a later age.
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Affiliation(s)
- Katharina N Diaye
- Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Str. 34, Freising, 85354, Germany
| | - Marcel Debong
- Aroma and Smell Research, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestr. 9, Erlangen, 91054, Germany
| | - Jürgen Behr
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Str. 34, Freising, 85354, Germany
| | - Sebastian Dirndorfer
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Str. 34, Freising, 85354, Germany
| | - Tara Duggan
- Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Str. 34, Freising, 85354, Germany
| | - Anja Beusch
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Str. 34, Freising, 85354, Germany
| | - Verena Schlagbauer
- Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Str. 34, Freising, 85354, Germany
| | - Corinna Dawid
- Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Str. 34, Freising, 85354, Germany
| | - Helene M Loos
- Aroma and Smell Research, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestr. 9, Erlangen, 91054, Germany.,Fraunhofer Institute for Process Engineering and Packaging IVV, Giggenhauser Str. 35, Freising, 85354, Germany
| | - Andrea Buettner
- Aroma and Smell Research, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestr. 9, Erlangen, 91054, Germany.,Fraunhofer Institute for Process Engineering and Packaging IVV, Giggenhauser Str. 35, Freising, 85354, Germany
| | - Roman Lang
- Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Str. 34, Freising, 85354, Germany.,Leibniz Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Str. 34, Freising, 85354, Germany
| | - Thomas Hofmann
- Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Str. 34, Freising, 85354, Germany
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Gotti C, Roux-Dalvai F, Joly-Beauparlant C, Mangnier L, Leclercq M, Droit A. Extensive and Accurate Benchmarking of DIA Acquisition Methods and Software Tools Using a Complex Proteomic Standard. J Proteome Res 2021; 20:4801-4814. [PMID: 34472865 DOI: 10.1021/acs.jproteome.1c00490] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Over the past decade, the data-independent acquisition mode has gained popularity for broad coverage of complex proteomes by LC-MS/MS and quantification of low-abundance proteins. However, there is no consensus in the literature on the best data acquisition parameters and processing tools to use for this specific application. Here, we present the most comprehensive comparison of DIA workflows on Orbitrap instruments published so far in the field of proteomics. Using a standard human 48 proteins mixture (UPS1-Sigma) at 8 different concentrations in an E. coli proteome background, we tested 36 workflows including 4 different DIA window acquisition schemes and 6 different software tools (DIA-NN, DIA-Umpire, OpenSWATH, ScaffoldDIA, Skyline, and Spectronaut) with or without the use of a DDA spectral library. On the basis of the number of proteins identified, quantification linearity and reproducibility, as well as sensitivity and specificity in 28 pairwise comparisons of different UPS1 concentrations, we summarize the major considerations and propose guidelines for choosing the DIA workflow best suited for LC-MS/MS proteomic analyses. Our 96 DIA raw files and software outputs have been deposited on ProteomeXchange for testing or developing new DIA processing tools.
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Affiliation(s)
- Clarisse Gotti
- Proteomics Platform, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada.,Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada
| | - Florence Roux-Dalvai
- Proteomics Platform, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada.,Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada
| | - Charles Joly-Beauparlant
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada
| | - Loïc Mangnier
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada
| | - Mickaël Leclercq
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada
| | - Arnaud Droit
- Proteomics Platform, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada.,Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada
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37
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SWATH-MS for prospective identification of protein blood biomarkers of rtPA-associated intracranial hemorrhage in acute ischemic stroke: a pilot study. Sci Rep 2021; 11:18765. [PMID: 34548538 PMCID: PMC8455557 DOI: 10.1038/s41598-021-97710-9] [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: 11/18/2020] [Accepted: 08/27/2021] [Indexed: 11/08/2022] Open
Abstract
Intravenous recombinant tissue plasminogen activator (rtPA) is, besides mechanical thrombectomy, the highest class evidence based reperfusion treatment of acute ischemic stroke (AIS). The biggest concern of the therapy is symptomatic intracranial hemorrhage (sICH), which occurs in 3-7% of all treated patients, and is associated with worse functional outcome. Finding a method of the powerful identification of patients at highest risk of sICH, in order to increase the percentage of stroke patients safely treated with rtPA, is one of the most important challenges in stroke research. To address this problem, we designed a complex project to identify blood, neuroimaging, and clinical biomarkers combined for prospective assessment of the risk of rtPA-associated ICH. In this paper we present results of blood proteomic and peptide analysis of pilot 41 AIS patients before rtPA administration (the test ICH group, n = 9 or the controls, without ICH, n = 32). We demonstrated that pre-treatment blood profiles of 15 proteins differ depending on whether the patients develop rtPA-associated ICH or not. SWATH-MS quantification of serum or plasma proteins might allow for robust selection of blood biomarkers to increase the prospective assessment of rtPA-associated ICH over that based solely on clinical and neuroimaging characteristics.
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38
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Zhang H, Bensaddek D. Narrow Precursor Mass Range for DIA-MS Enhances Protein Identification and Quantification in Arabidopsis. Life (Basel) 2021; 11:982. [PMID: 34575131 PMCID: PMC8469718 DOI: 10.3390/life11090982] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/03/2021] [Accepted: 09/15/2021] [Indexed: 12/02/2022] Open
Abstract
Data independent acquisition-mass spectrometry (DIA-MS) is becoming widely utilised for robust and accurate quantification of samples in quantitative proteomics. Here, we describe the systematic evaluation of the effects of DIA precursor mass range on total protein identification and quantification. We show that a narrow mass range of precursors (~250 m/z) for DIA-MS enables a higher number of protein identifications. Subsequent application of DIA with narrow precursor range (from 400 to 650 m/z) on an Arabidopsis sample with spike-in known proteins identified 34.7% more proteins than in conventional DIA (cDIA) with a wide precursor range of 400-1200 m/z. When combining several DIA-MS analyses with narrow precursor ranges (i.e., 400-650, 650-900 and 900-1200 m/z), we were able to quantify 10,099 protein groups with a median coefficient of variation of <6%. These findings represent a 54.7% increase in the number of proteins quantified than with cDIA analysis. This is particularly important for low abundance proteins, as exemplified by the six-protein mix spike-in. In cDIA only five out of the six-protein mix were quantified while our approach allowed accurate quantitation of all six proteins.
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Affiliation(s)
| | - Dalila Bensaddek
- Core Labs, King Abdullah University of Science and Technology, Thuwal 23500-6900, Saudi Arabia;
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39
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de Albuquerque Cavalcanti G, Moreira Borges R, Reis Alves Carneiro G, Costa Padilha M, Gualberto Pereira HM. Variable Data Independent Acquisition and Data Mining Exploring Feature-Based Molecular Networking Analysis for Untargeted Screening of Synthetic Cannabinoids in Oral Fluid. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2417-2424. [PMID: 34399051 DOI: 10.1021/jasms.1c00124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Novel psychoactive substances (NPS) are constantly emerging in the drug market, and synthetic cannabinoids (SCs) are included in this NPS family. Forensic laboratories often struggle with these continually emerging SCs, forcing them to develop an untargeted workflow to incorporate these psychoactive drugs in their procedures. Usually, forensic laboratories select analytical methods based on targeted mass spectrometry (MS) technologies for strictly tracking already known NPS. The appropriate way to tackle unknown substances is to develop pipelines for untargeted analysis that include LC-HRMS analytical methods and data analysis. Once established, this strategy would allow drug testing laboratories to be always one step ahead of the new trends concerning the "designer drugs" market. To address this challenge an untargeted workflow based on mass spectrometry data acquisition and data analysis was developed to detect SCs in oral fluid (OF) samples at a low concentration range. The samples were extracted by mixed-mode solid-phase extraction and analyzed by Liquid Chromatography - High-Resolution Mass Spectrometry (LC-HRMS). Tandem mass spectra (MS2) were recorded performing a variable isolation width across a mass range of all theoretical precursor ions (vDIA) after the chromatographic separation. After raw data processing with the MSDial software, the deconvoluted features were sent to GNPS for Feature-Based Molecular Networking (FBMN) construction for nontargeted data mining. The FBMN analysis created a unique integrated network for most of the SCs assessed in the OF at a low level (20 ng/mL). These results demonstrate the potential of an untargeted approach to detect different derivatives of SCs at trace levels for forensic applications.
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Affiliation(s)
- Gustavo de Albuquerque Cavalcanti
- Brazilian Doping Control Laboratory (LBCD), Chemistry Institute, Federal University of Rio de Janeiro (UFRJ), 21941-598 Rio de Janeiro, RJ, Brazil
| | - Ricardo Moreira Borges
- Walter Mors Institute of Research on Natural Products (IPPN), Federal University of Rio de Janeiro (UFRJ), 21941-902 Rio de Janeiro, RJ, Brazil
| | - Gabriel Reis Alves Carneiro
- Brazilian Doping Control Laboratory (LBCD), Chemistry Institute, Federal University of Rio de Janeiro (UFRJ), 21941-598 Rio de Janeiro, RJ, Brazil
| | - Monica Costa Padilha
- Brazilian Doping Control Laboratory (LBCD), Chemistry Institute, Federal University of Rio de Janeiro (UFRJ), 21941-598 Rio de Janeiro, RJ, Brazil
| | - Henrique Marcelo Gualberto Pereira
- Brazilian Doping Control Laboratory (LBCD), Chemistry Institute, Federal University of Rio de Janeiro (UFRJ), 21941-598 Rio de Janeiro, RJ, Brazil
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40
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Fiołka MJ, Czaplewska P, Wójcik-Mieszawska S, Lewandowska A, Lewtak K, Sofińska-Chmiel W, Buchwald T. Metabolic, structural, and proteomic changes in Candida albicans cells induced by the protein-carbohydrate fraction of Dendrobaena veneta coelomic fluid. Sci Rep 2021; 11:16711. [PMID: 34408181 PMCID: PMC8373886 DOI: 10.1038/s41598-021-96093-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/02/2021] [Indexed: 01/14/2023] Open
Abstract
The isolated protein-polysaccharide fraction (AAF) from the coelomic fluid of Dendrobaena veneta earthworm shows effective activity against Candida albicans yeast. Fungal cells of the clinical strain after incubation with the active fraction were characterized by disturbed cell division and different morphological forms due to the inability to separate the cells from each other. Staining of the cells with acridine orange revealed a change in the pH of the AAF-treated cells. It was observed that, after the AAF treatment, the mitochondrial DNA migrated towards the nuclear DNA, whereupon both merged into a single nuclear structure, which preceded the apoptotic process. Cells with a large nucleus were imaged with the scanning electron cryomicroscopy (Cryo-SEM) technique, while enlarged mitochondria and the degeneration of cell structures were shown by transmission electron microscopy (TEM). The loss of the correct cell shape and cell wall integrity was visualized by both the TEM and SEM techniques. Mass spectrometry and relative quantitative SWATH MS analysis were used to determine the reaction of the C. albicans proteome to the components of the AAF fraction. AAF was observed to influence the expression of mitochondrial and oxidative stress proteins. The oxidative stress in C. albicans cells caused by the action of AAF was demonstrated by fluorescence microscopy, proteomic methods, and XPS spectroscopy. The secondary structure of AAF proteins was characterized by Raman spectroscopy. Analysis of the elemental composition of AAF confirmed the homogeneity of the preparation. The observed action of AAF, which targets not only the cell wall but also the mitochondria, makes the preparation a potential antifungal drug killing the cells of the C. albicans pathogen through apoptosis.
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Affiliation(s)
- Marta J Fiołka
- Department of Immunobiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland.
| | - Paulina Czaplewska
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Sylwia Wójcik-Mieszawska
- Department of Immunobiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Aleksandra Lewandowska
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Kinga Lewtak
- Department of Cell Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Weronika Sofińska-Chmiel
- Analytical Laboratory, Institute of Chemical Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Tomasz Buchwald
- Faculty of Materials Science and Technical Physics, Institute of Materials Research and Quantum Engineering, Poznan University of Technology, Poznań, Poland
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41
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Serrano-Blesa E, Porter A, Lendrem DW, Pitzalis C, Barton A, Treumann A, Isaacs JD. Robust optimization of SWATH-MS workflow for human blood serum proteome analysis using a quality by design approach. Clin Proteomics 2021; 18:20. [PMID: 34384350 PMCID: PMC8359389 DOI: 10.1186/s12014-021-09323-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 07/21/2021] [Indexed: 11/13/2022] Open
Abstract
Background It is not enough to optimize proteomics assays. It is critical those assays are robust to operating conditions. Without robust assays, proteomic biomarkers are unlikely to translate readily into the clinic. This study outlines a structured approach to the identification of a robust operating window for proteomics assays and applies that method to Sequential Window Acquisition of all Theoretical Spectra Mass Spectroscopy (SWATH-MS). Methods We used a sequential quality by design approach exploiting a fractional screening design to first identify critical SWATH-MS parameters, then using response surface methods to identify a robust operating window with good reproducibility, before validating those settings in a separate validation study. Results The screening experiment identified two critical SWATH-MS parameters. We modelled the number of proteins and reproducibility as a function of those parameters identifying an operating window permitting robust maximization of the number of proteins quantified in human serum. In a separate validation study, these settings were shown to give good proteome-wide coverage and high quantification reproducibility. Conclusions Using design of experiments permits identification of a robust operating window for SWATH-MS. The method gives a good understanding of proteomics assays and greater data-driven confidence in SWATH-MS performance. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-021-09323-z.
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Affiliation(s)
- Edith Serrano-Blesa
- National Institute of Health Research Newcastle Biomedical Research Centre and the Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew Porter
- Newcastle University Protein and Proteome Facility, Newcastle upon Tyne, UK
| | - Dennis W Lendrem
- National Institute of Health Research Newcastle Biomedical Research Centre and the Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Costantino Pitzalis
- Centre for Experimental Medicine and Rheumatology, Queen Mary University of London, London, UK
| | - Anne Barton
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre,, The University of Manchester, Manchester, UK
| | - Achim Treumann
- Newcastle University Protein and Proteome Facility, Newcastle upon Tyne, UK
| | - John D Isaacs
- National Institute of Health Research Newcastle Biomedical Research Centre and the Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK. .,Musculoskeletal Unit, Freeman Hospital, Newcastle upon Tyne NHS Foundation Trust, Newcastle upon Tyne, UK.
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42
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Lewandowska AE, Fel A, Thiel M, Czaplewska P, Łukaszuk K, Wiśniewski JR, Ołdziej S. Compatibility of Distinct Label-Free Proteomic Workflows in Absolute Quantification of Proteins Linked to the Oocyte Quality in Human Follicular Fluid. Int J Mol Sci 2021; 22:7415. [PMID: 34299044 PMCID: PMC8304916 DOI: 10.3390/ijms22147415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 01/02/2023] Open
Abstract
We present two separate label-free quantitative workflows based on different high-resolution mass spectrometers and LC setups, which are termed after the utilized instrument: Quad-Orbitrap (nano-LC) and Triple Quad-TOF (micro-LC) and their directed adaptation toward the analysis of human follicular fluid proteome. We identified about 1000 proteins in each distinct workflow using various sample preparation methods. With assistance of the Total Protein Approach, we were able to obtain absolute protein concentrations for each workflow. In a pilot study of twenty samples linked to diverse oocyte quality status from four donors, 455 and 215 proteins were quantified by the Quad-Orbitrap and Triple Quad-TOF workflows, respectively. The concentration values obtained from both workflows correlated to a significant degree. We found reasonable agreement of both workflows in protein fold changes between tested groups, resulting in unified lists of 20 and 22 proteins linked to oocyte maturity and blastocyst development, respectively. The Quad-Orbitrap workflow was best suited for an in-depth analysis without the need of extensive fractionation, especially of low abundant proteome, whereas the Triple Quad-TOF workflow allowed a more robust approach with a greater potential to increase in effectiveness with the growing number of analyzed samples after the initial effort of building a comprehensive spectral library.
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Affiliation(s)
- Aleksandra E. Lewandowska
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland; (A.F.); (M.T.); (P.C.)
| | - Anna Fel
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland; (A.F.); (M.T.); (P.C.)
| | - Marcel Thiel
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland; (A.F.); (M.T.); (P.C.)
| | - Paulina Czaplewska
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland; (A.F.); (M.T.); (P.C.)
| | - Krzysztof Łukaszuk
- INVICTA Fertility and Reproductive Center, Polna 64, 81-740 Sopot, Poland;
- Department of Obstetrics and Gynecological Nursing, Faculty of Health Sciences, Medical University of Gdańsk, Dębinki 7, 80-211 Gdańsk, Poland
| | - Jacek R. Wiśniewski
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany;
| | - Stanisław Ołdziej
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland; (A.F.); (M.T.); (P.C.)
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43
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Kleis J, Hess C, Germerott T, Roehrich J. Sensitive Screening of New Psychoactive Substances in Serum Using Liquid-Chromatography Quadrupole Time-of-Flight Mass Spectrometry. J Anal Toxicol 2021; 46:592-599. [PMID: 34125215 DOI: 10.1093/jat/bkab072] [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: 04/19/2021] [Revised: 06/10/2021] [Accepted: 06/12/2021] [Indexed: 01/18/2023] Open
Abstract
Analysis of new psychoactive substances (NPS) still pose a challenge for many institutions due to the number of available substances and the constantly changing drug market. Both new and well-known substances keep appearing and disappearing on the market, making it hard to adapt analytical methods in a timely manner. In this study we developed a qualitative screening approach for serum samples by means of liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF-MS). Samples were measured in data-dependent auto-MS/MS mode and identified by fragment spectra comparison, retention time and accurate mass. Approximately 500 NPS, including 195 synthetic cannabinoids, 180 stimulants, 86 hallucinogens, 26 benzodiazepines and 7 others were investigated. Serum samples were fortified to 1 ng/mL and 10 ng/mL concentrations to estimate approximate limits of identification. Samples were extracted using solid-phase extraction with non-endcapped C18 material and elution in two consecutive steps. Benzodiazepines were eluted in the first step, while substances of other NPS subclasses were distributed among both extracts. To determine limits of identification, both extracts were combined. 96 % (470/492) of investigated NPS were detected in 10 ng/mL samples and 88 % (432/492) were detected in 1 ng/mL samples. Stimulants stood out with higher limits of identification, possibly due to instability of certain methcathinone derivatives. However, considering relevant blood concentrations, the method provided sufficient sensitivity for stimulants as well as other NPS subclasses. Data-dependent acquisition was proven to provide high sensitivity and reliability when combined with an information-dependent preferred list, without losing its untargeted operation principle. Summarizing, the developed method fulfilled its purpose as a sensitive untargeted screening for serum samples and allows uncomplicated expansion of the spectral library to include thousands of targets.
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Affiliation(s)
- J Kleis
- Institute of Forensic Medicine, Forensic Toxicology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - C Hess
- Institute of Forensic Medicine, Forensic Toxicology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - T Germerott
- Institute of Forensic Medicine, Forensic Toxicology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - J Roehrich
- Institute of Forensic Medicine, Forensic Toxicology, Johannes Gutenberg University Mainz, Mainz, Germany
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44
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Bian J, Sze YH, Tse DYY, To CH, McFadden SA, Lam CSY, Li KK, Lam TC. SWATH Based Quantitative Proteomics Reveals Significant Lipid Metabolism in Early Myopic Guinea Pig Retina. Int J Mol Sci 2021; 22:4721. [PMID: 33946922 PMCID: PMC8124159 DOI: 10.3390/ijms22094721] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/22/2021] [Accepted: 04/25/2021] [Indexed: 12/14/2022] Open
Abstract
Most of the previous myopic animal studies employed a single-candidate approach and lower resolution proteomics approaches that were difficult to detect minor changes, and generated limited systems-wide biological information. Hence, a complete picture of molecular events in the retina involving myopic development is lacking. Here, to investigate comprehensive retinal protein alternations and underlying molecular events in the early myopic stage, we performed a data-independent Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH) based proteomic analysis coupled with different bioinformatics tools in pigmented guinea pigs after 4-day lens-induced myopia (LIM). Myopic eyes compared to untreated contralateral control eyes caused significant changes in refractive error and choroid thickness (p < 0.05, n = 5). Relative elongation of axial length and the vitreous chamber depth were also observed. Using pooled samples from all individuals (n = 10) to build a species-specific retinal ion library for SWATH analysis, 3202 non-redundant proteins (with 24,616 peptides) were identified at 1% global FDR. For quantitative analysis, the 10 individual retinal samples (5 pairs) were analyzed using a high resolution Triple-TOF 6600 mass spectrometry (MS) with technical replicates. In total, 37 up-regulated and 21 down-regulated proteins were found significantly changed after LIM treatment (log2 ratio (T/C) > 0.26 or < -0.26; p ≤ 0.05). Data are accepted via ProteomeXchange with identifier PXD025003. Through Ingenuity Pathways Analysis (IPA), "lipid metabolism" was found as the top function associated with the differentially expressed proteins. Based on the protein abundance and peptide sequences, expression patterns of two regulated proteins (SLC6A6 and PTGES2) identified in this pathway were further successfully validated with high confidence (p < 0.05) using a novel Multiple Reaction Monitoring (MRM) assay on a QTRAP 6500+ MS. In summary, through an integrated discovery and targeted proteomic approach, this study serves as the first report to detect and confirm novel retinal protein changes and significant biological functions in the early LIM mammalian guinea pigs. The study provides new workflow and insights for further research to myopia control.
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Affiliation(s)
- Jingfang Bian
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
| | - Ying-Hon Sze
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
| | - Dennis Yan-Yin Tse
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
| | - Chi-Ho To
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
| | - Sally A. McFadden
- School of Psychology, College of Engineering, Science and the Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Carly Siu-Yin Lam
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
| | - King-Kit Li
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
| | - Thomas Chuen Lam
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
- Shenzhen Research Institute, The Hong Kong Polytechnic University, Shenzhen 518052, China
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Network mapping of primary CD34+ cells by Ampliseq based whole transcriptome targeted resequencing identifies unexplored differentiation regulatory relationships. PLoS One 2021; 16:e0246107. [PMID: 33544756 PMCID: PMC7864404 DOI: 10.1371/journal.pone.0246107] [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: 03/30/2020] [Accepted: 01/13/2021] [Indexed: 12/04/2022] Open
Abstract
With the exception of a few master transcription factors, regulators of neutrophil maturation are poorly annotated in the intermediate phenotypes between the granulocyte-macrophage progenitor (GMP) and the mature neutrophil phenotype. Additional challenges in identifying gene expression regulators in differentiation pathways relate to challenges wherein starting cell populations are heterogeneous in lineage potential and development, are spread across various states of quiescence, as well as sample quality and input limitations. These factors contribute to data variability make it difficult to draw simple regulatory inferences. In response we have applied a multi-omics approach using primary blood progenitor cells primed for homogeneous proliferation and granulocyte differentiation states which combines whole transcriptome resequencing (Ampliseq RNA) supported by droplet digital PCR (ddPCR) validation and mass spectrometry-based proteomics in a hypothesis-generation study of neutrophil differentiation pathways. Primary CD34+ cells isolated from human cord blood were first precultured in non-lineage driving medium to achieve an active, proliferating phenotype from which a neutrophil primed progenitor was isolated and cultured in neutrophil lineage supportive medium. Samples were then taken at 24-hour intervals over 9 days and analysed by Ampliseq RNA and mass spectrometry. The Ampliseq dataset depth, breadth and quality allowed for several unexplored transcriptional regulators and ncRNAs to be identified using a combinatorial approach of hierarchical clustering, enriched transcription factor binding motifs, and network mapping. Network mapping in particular increased comprehension of neutrophil differentiation regulatory relationships by implicating ARNT, NHLH1, PLAG1, and 6 non-coding RNAs associated with PU.1 regulation as cell-engineering targets with the potential to increase total neutrophil culture output. Overall, this study develops and demonstrates an effective new hypothesis generation methodology for transcriptome profiling during differentiation, thereby enabling identification of novel gene targets for editing interventions.
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Peper J, Kownatzki-Danger D, Weninger G, Seibertz F, Pronto JRD, Sutanto H, Pacheu-Grau D, Hindmarsh R, Brandenburg S, Kohl T, Hasenfuss G, Gotthardt M, Rog-Zielinska EA, Wollnik B, Rehling P, Urlaub H, Wegener J, Heijman J, Voigt N, Cyganek L, Lenz C, Lehnart SE. Caveolin3 Stabilizes McT1-Mediated Lactate/Proton Transport in Cardiomyocytes. Circ Res 2021; 128:e102-e120. [PMID: 33486968 DOI: 10.1161/circresaha.119.316547] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Jonas Peper
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen (J.P., D.K.-D., G.W., S.B., T.K., G.H., J.W., S.E.L.), University Medical Center Göttingen.,Cardiology & Pneumology (J.P., D.K.-D., G.W., R.H., S.B., T.K., G.H., J.W., L.C., S.E.L.), University Medical Center Göttingen
| | - Daniel Kownatzki-Danger
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen (J.P., D.K.-D., G.W., S.B., T.K., G.H., J.W., S.E.L.), University Medical Center Göttingen.,Cardiology & Pneumology (J.P., D.K.-D., G.W., R.H., S.B., T.K., G.H., J.W., L.C., S.E.L.), University Medical Center Göttingen
| | - Gunnar Weninger
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen (J.P., D.K.-D., G.W., S.B., T.K., G.H., J.W., S.E.L.), University Medical Center Göttingen.,Cardiology & Pneumology (J.P., D.K.-D., G.W., R.H., S.B., T.K., G.H., J.W., L.C., S.E.L.), University Medical Center Göttingen
| | - Fitzwilliam Seibertz
- Institute of Pharmacology and Toxicology (F.S., J.R.D.P., N.V.), University Medical Center Göttingen.,DZHK (German Centre for Cardiovascular Research), partner site Göttingen (F.S., S.B., T.K., G.H., J.W., N.V., L.C., S.E.L.)
| | - Julius Ryan D Pronto
- Institute of Pharmacology and Toxicology (F.S., J.R.D.P., N.V.), University Medical Center Göttingen
| | - Henry Sutanto
- Cardiology, Cardiovascular Research Institute Maastricht, Maastricht University (H.S., J.H.)
| | - David Pacheu-Grau
- Cellular Biochemistry, University Medical Center, Georg-August-University (D.P.G., P.R.)
| | - Robin Hindmarsh
- Cardiology & Pneumology (J.P., D.K.-D., G.W., R.H., S.B., T.K., G.H., J.W., L.C., S.E.L.), University Medical Center Göttingen
| | - Sören Brandenburg
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen (J.P., D.K.-D., G.W., S.B., T.K., G.H., J.W., S.E.L.), University Medical Center Göttingen.,Cardiology & Pneumology (J.P., D.K.-D., G.W., R.H., S.B., T.K., G.H., J.W., L.C., S.E.L.), University Medical Center Göttingen.,DZHK (German Centre for Cardiovascular Research), partner site Göttingen (F.S., S.B., T.K., G.H., J.W., N.V., L.C., S.E.L.)
| | - Tobias Kohl
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen (J.P., D.K.-D., G.W., S.B., T.K., G.H., J.W., S.E.L.), University Medical Center Göttingen.,Cardiology & Pneumology (J.P., D.K.-D., G.W., R.H., S.B., T.K., G.H., J.W., L.C., S.E.L.), University Medical Center Göttingen.,DZHK (German Centre for Cardiovascular Research), partner site Göttingen (F.S., S.B., T.K., G.H., J.W., N.V., L.C., S.E.L.)
| | - Gerd Hasenfuss
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen (J.P., D.K.-D., G.W., S.B., T.K., G.H., J.W., S.E.L.), University Medical Center Göttingen.,Cardiology & Pneumology (J.P., D.K.-D., G.W., R.H., S.B., T.K., G.H., J.W., L.C., S.E.L.), University Medical Center Göttingen.,DZHK (German Centre for Cardiovascular Research), partner site Göttingen (F.S., S.B., T.K., G.H., J.W., N.V., L.C., S.E.L.).,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen (G.H., B.W., P.R., N.V., S.E.L.)
| | - Michael Gotthardt
- Neuromuscular and Cardiovascular Cell Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin (M.G.).,Cardiology, Virchow Klinikum, Charité-University Medicine, Berlin (M.G.).,DZHK (German Center for Cardiovascular Research), partner site Berlin (M.G.)
| | - Eva A Rog-Zielinska
- University Heart Center, Faculty of Medicine, University of Freiburg (E.A.R.-Z.)
| | - Bernd Wollnik
- Institute of Human Genetics (B.W.), University Medical Center Göttingen.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen (G.H., B.W., P.R., N.V., S.E.L.)
| | - Peter Rehling
- Cellular Biochemistry, University Medical Center, Georg-August-University (D.P.G., P.R.).,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen (G.H., B.W., P.R., N.V., S.E.L.)
| | - Henning Urlaub
- Bioanalytics, Institute of Clinical Chemistry (H.U., C.L.), University Medical Center Göttingen.,Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen (H.U., C.L.)
| | - Jörg Wegener
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen (J.P., D.K.-D., G.W., S.B., T.K., G.H., J.W., S.E.L.), University Medical Center Göttingen.,Cardiology & Pneumology (J.P., D.K.-D., G.W., R.H., S.B., T.K., G.H., J.W., L.C., S.E.L.), University Medical Center Göttingen.,DZHK (German Centre for Cardiovascular Research), partner site Göttingen (F.S., S.B., T.K., G.H., J.W., N.V., L.C., S.E.L.)
| | - Jordi Heijman
- Cardiology, Cardiovascular Research Institute Maastricht, Maastricht University (H.S., J.H.)
| | - Niels Voigt
- Institute of Pharmacology and Toxicology (F.S., J.R.D.P., N.V.), University Medical Center Göttingen.,DZHK (German Centre for Cardiovascular Research), partner site Göttingen (F.S., S.B., T.K., G.H., J.W., N.V., L.C., S.E.L.).,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen (G.H., B.W., P.R., N.V., S.E.L.)
| | - Lukas Cyganek
- DZHK (German Centre for Cardiovascular Research), partner site Göttingen (F.S., S.B., T.K., G.H., J.W., N.V., L.C., S.E.L.)
| | - Christof Lenz
- Bioanalytics, Institute of Clinical Chemistry (H.U., C.L.), University Medical Center Göttingen.,Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen (H.U., C.L.)
| | - Stephan E Lehnart
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen (J.P., D.K.-D., G.W., S.B., T.K., G.H., J.W., S.E.L.), University Medical Center Göttingen.,Cardiology & Pneumology (J.P., D.K.-D., G.W., R.H., S.B., T.K., G.H., J.W., L.C., S.E.L.), University Medical Center Göttingen.,DZHK (German Centre for Cardiovascular Research), partner site Göttingen (F.S., S.B., T.K., G.H., J.W., N.V., L.C., S.E.L.).,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen (G.H., B.W., P.R., N.V., S.E.L.).,BioMET, Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore (S.E.L.)
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van der Laan T, Boom I, Maliepaard J, Dubbelman AC, Harms AC, Hankemeier T. Data-Independent Acquisition for the Quantification and Identification of Metabolites in Plasma. Metabolites 2020; 10:metabo10120514. [PMID: 33353236 PMCID: PMC7766927 DOI: 10.3390/metabo10120514] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/13/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023] Open
Abstract
A popular fragmentation technique for non-targeted analysis is called data-independent acquisition (DIA), because it provides fragmentation data for all analytes in a specific mass range. In this work, we demonstrated the strengths and weaknesses of DIA. Two types of chromatography (fractionation/3 min and hydrophilic interaction liquid chromatography (HILIC)/18 min) and three DIA protocols (variable sequential window acquisition of all theoretical mass spectra (SWATH), fixed SWATH and MSALL) were used to evaluate the performance of DIA. Our results show that fast chromatography and MSALL often results in product ion overlap and complex MS/MS spectra, which reduces the quantitative and qualitative power of these DIA protocols. The combination of SWATH and HILIC allowed for the correct identification of 20 metabolites using the NIST library. After SWATH window customization (i.e., variable SWATH), we were able to quantify ten structural isomers with a mean accuracy of 103% (91-113%). The robustness of the variable SWATH and HILIC method was demonstrated by the accurate quantification of these structural isomers in 10 highly diverse blood samples. Since the combination of variable SWATH and HILIC results in good quantitative and qualitative fragmentation data, it is promising for both targeted and untargeted platforms. This should decrease the number of platforms needed in metabolomics and increase the value of a single analysis.
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Karuna M P, Witte L, Linnemannstoens K, Choezom D, Danieli-Mackay A, Honemann-Capito M, Gross JC. Phosphorylation of Ykt6 SNARE Domain Regulates Its Membrane Recruitment and Activity. Biomolecules 2020; 10:biom10111560. [PMID: 33207719 PMCID: PMC7696345 DOI: 10.3390/biom10111560] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/17/2022] Open
Abstract
Sensitive factor attachment protein receptors (SNARE) proteins are important mediators of protein trafficking that regulate the membrane fusion of specific vesicle populations and their target organelles. The SNARE protein Ykt6 lacks a transmembrane domain and attaches to different organelle membranes. Mechanistically, Ykt6 activity is thought to be regulated by a conformational change from a closed cytosolic form to an open membrane-bound form, yet the mechanism that regulates this transition is unknown. We identified phosphorylation sites in the SNARE domain of Ykt6 that mediate Ykt6 membrane recruitment and are essential for cellular growth. Using proximity-dependent labeling and membrane fractionation, we found that phosphorylation regulates Ykt6 conversion from a closed to an open conformation. This conformational switch recruits Ykt6 to several organelle membranes, where it functionally regulates the trafficking of Wnt proteins and extracellular vesicle secretion in a concentration-dependent manner. We propose that phosphorylation of its SNARE domain leads to a conformational switch from a cytosolic, auto-inhibited Ykt6 to an active SNARE at different membranes.
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Affiliation(s)
- Pradhipa Karuna M
- Hematology and Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (P.K.M.); (L.W.); (K.L.); (D.C.); (A.D.-M.); (M.H.-C.)
- Developmental Biochemistry, University Medical Center Goettingen, 37077 Goettingen, Germany
| | - Leonie Witte
- Hematology and Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (P.K.M.); (L.W.); (K.L.); (D.C.); (A.D.-M.); (M.H.-C.)
- Developmental Biochemistry, University Medical Center Goettingen, 37077 Goettingen, Germany
| | - Karen Linnemannstoens
- Hematology and Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (P.K.M.); (L.W.); (K.L.); (D.C.); (A.D.-M.); (M.H.-C.)
- Developmental Biochemistry, University Medical Center Goettingen, 37077 Goettingen, Germany
| | - Dolma Choezom
- Hematology and Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (P.K.M.); (L.W.); (K.L.); (D.C.); (A.D.-M.); (M.H.-C.)
- Developmental Biochemistry, University Medical Center Goettingen, 37077 Goettingen, Germany
| | - Adi Danieli-Mackay
- Hematology and Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (P.K.M.); (L.W.); (K.L.); (D.C.); (A.D.-M.); (M.H.-C.)
- Developmental Biochemistry, University Medical Center Goettingen, 37077 Goettingen, Germany
| | - Mona Honemann-Capito
- Hematology and Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (P.K.M.); (L.W.); (K.L.); (D.C.); (A.D.-M.); (M.H.-C.)
- Developmental Biochemistry, University Medical Center Goettingen, 37077 Goettingen, Germany
| | - Julia Christina Gross
- Hematology and Oncology, University Medical Center Goettingen, 37077 Goettingen, Germany; (P.K.M.); (L.W.); (K.L.); (D.C.); (A.D.-M.); (M.H.-C.)
- Developmental Biochemistry, University Medical Center Goettingen, 37077 Goettingen, Germany
- HMU Health and Medical University Potsdam, 14471 Potsdam, Germany
- Correspondence:
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49
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Hellinger JW, Schömel F, Buse JV, Lenz C, Bauerschmitz G, Emons G, Gründker C. Identification of drivers of breast cancer invasion by secretome analysis: insight into CTGF signaling. Sci Rep 2020; 10:17889. [PMID: 33087801 PMCID: PMC7578015 DOI: 10.1038/s41598-020-74838-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022] Open
Abstract
An altered consistency of tumor microenvironment facilitates the progression of the tumor towards metastasis. Here we combine data from secretome and proteome analysis using mass spectrometry with microarray data from mesenchymal transformed breast cancer cells (MCF-7-EMT) to elucidate the drivers of epithelial-mesenchymal transition (EMT) and cell invasion. Suppression of connective tissue growth factor (CTGF) reduced invasion in 2D and 3D invasion assays and expression of transforming growth factor-beta-induced protein ig-h3 (TGFBI), Zinc finger E-box-binding homeobox 1 (ZEB1) and lysyl oxidase (LOX), while the adhesion of cell-extracellular matrix (ECM) in mesenchymal transformed breast cancer cells is increased. In contrast, an enhanced expression of CTGF leads to an increased 3D invasion, expression of fibronectin 1 (FN1), secreted protein acidic and cysteine rich (SPARC) and CD44 and a reduced cell ECM adhesion. Gonadotropin-releasing hormone (GnRH) agonist Triptorelin reduces CTGF expression in a Ras homolog family member A (RhoA)-dependent manner. Our results suggest that CTGF drives breast cancer cell invasion in vitro and therefore could be an attractive therapeutic target for drug development to prevent the spread of breast cancer.
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Affiliation(s)
- Johanna W Hellinger
- Department of Gynecology and Obstetrics, University Medicine Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Franziska Schömel
- Department of Gynecology and Obstetrics, University Medicine Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Judith V Buse
- Department of Gynecology and Obstetrics, University Medicine Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Christof Lenz
- Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Gerd Bauerschmitz
- Department of Gynecology and Obstetrics, University Medicine Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Günter Emons
- Department of Gynecology and Obstetrics, University Medicine Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Carsten Gründker
- Department of Gynecology and Obstetrics, University Medicine Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany.
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50
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Cai X, Ge W, Yi X, Sun R, Zhu J, Lu C, Sun P, Zhu T, Ruan G, Yuan C, Liang S, Lyu M, Huang S, Zhu Y, Guo T. PulseDIA: Data-Independent Acquisition Mass Spectrometry Using Multi-Injection Pulsed Gas-Phase Fractionation. J Proteome Res 2020; 20:279-288. [PMID: 32975123 DOI: 10.1021/acs.jproteome.0c00381] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The performance of data-independent acquisition (DIA) mass spectrometry (MS) depends on the separation efficiency of peptide precursors. In Orbitrap-based mass spectrometers, separation efficiency of peptide precursors is limited by the relatively slow scanning rate compared to time of flight (TOF)-based MS. Here, we present PulseDIA, a multi-injection gas-phase fractionation (GPF) strategy for enhanced DIA-MS. This is achieved by equally dividing the conventional DIA analysis covering the entire mass range into multiple injections for DIA analyses with complementary windows. Using mouse liver digests, the PulseDIA method identified up to 50% more peptides and 29% more protein groups than that by conventional DIA with the same length of effective gradient time. Compared to conventional multi-injection GPF, PusleDIA exhibited higher flexibility and identified up to 18% more peptides and 8% more protein groups using two injections. The gain of peptides per effective time unit was the highest in PulseDIA compared to conventional DIA and GPF. We further applied the PulseDIA method to profile the proteome of 18 human tissue samples (benign and malignant) from nine cholangiocarcinoma (CCA) patients. PulseDIA identified 7796 protein groups in these CCA samples, with a 14% increase of protein group identification compared to the conventional DIA method. The missing value for protein matrix dropped by 7% using PulseDIA compared to DIA. A total of 681 significantly altered proteins were detected in CCA samples using PulseDIA, including several dysregulated proteins, which were absent in the conventional DIA analysis. Taken together, we present PulseDIA as an enhanced DIA-MS method with improved sensitivity and reproducibility.
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Affiliation(s)
- Xue Cai
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Weigang Ge
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Xiao Yi
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Rui Sun
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Jiang Zhu
- Center for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Cong Lu
- Center for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Ping Sun
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Tiansheng Zhu
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Guan Ruan
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Chunhui Yuan
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Shuang Liang
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Mengge Lyu
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Shiang Huang
- Center for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Yi Zhu
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Tiannan Guo
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
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