1
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Gali A, Bijnsdorp IV, Piersma SR, Pham TV, Gutiérrez-Galindo E, Kühnel F, Tsolakos N, Jimenez CR, Hausser A, Alexopoulos LG. Protein kinase D drives the secretion of invasion mediators in triple-negative breast cancer cell lines. iScience 2024; 27:108958. [PMID: 38323010 PMCID: PMC10844833 DOI: 10.1016/j.isci.2024.108958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 11/28/2023] [Accepted: 01/15/2024] [Indexed: 02/08/2024] Open
Abstract
The protein kinase D (PKD) family members regulate the fission of cargo vesicles at the Golgi complex and play a pro-oncogenic role in triple-negative breast cancer (TNBC). Whether PKD facilitates the secretion of tumor-promoting factors in TNBC, however, is still unknown. Using the pharmacological inhibition of PKD activity and siRNA-mediated depletion of PKD2 and PKD3, we identified the PKD-dependent secretome of the TNBC cell lines MDA-MB-231 and MDA-MB-468. Mass spectrometry-based proteomics and antibody-based assays revealed a significant downregulation of extracellular matrix related proteins and pro-invasive factors such as LIF, MMP-1, MMP-13, IL-11, M-CSF and GM-CSF in PKD-perturbed cells. Notably, secretion of these proteins in MDA-MB-231 cells was predominantly controlled by PKD2 and enhanced spheroid invasion. Consistently, PKD-dependent secretion of pro-invasive factors was more pronounced in metastatic TNBC cell lines. Our study thus uncovers a novel role of PKD2 in releasing a pro-invasive secretome.
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Affiliation(s)
- Alexia Gali
- Biomedical Systems Laboratory, National Technical University of Athens, 15780 Athens, Greece
- Protavio Ltd, Demokritos Science Park, 15341 Athens, Greece
| | - Irene V. Bijnsdorp
- Department of Urology, Cancer Center Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, de Boelelaan 1117, Amsterdam 1081 HV, the Netherlands
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, OncoProteomics Laboratory, de Boelelaan 1117, , Amsterdam 1081 HV, the Netherlands
| | - Sander R. Piersma
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, OncoProteomics Laboratory, de Boelelaan 1117, , Amsterdam 1081 HV, the Netherlands
| | - Thang V. Pham
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, OncoProteomics Laboratory, de Boelelaan 1117, , Amsterdam 1081 HV, the Netherlands
| | | | - Fiona Kühnel
- Institute of Cell Biology and Immunology, University of Stuttgart, 70569 Stuttgart, Germany
| | - Nikos Tsolakos
- Protavio Ltd, Demokritos Science Park, 15341 Athens, Greece
| | - Connie R. Jimenez
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, OncoProteomics Laboratory, de Boelelaan 1117, , Amsterdam 1081 HV, the Netherlands
| | - Angelika Hausser
- Institute of Cell Biology and Immunology, University of Stuttgart, 70569 Stuttgart, Germany
- Stuttgart Research Center for Systems Biology, University of Stuttgart, 70569 Stuttgart, Germany
| | - Leonidas G. Alexopoulos
- Biomedical Systems Laboratory, National Technical University of Athens, 15780 Athens, Greece
- Protavio Ltd, Demokritos Science Park, 15341 Athens, Greece
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2
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Fernandez M, Callegari EA, Paez MD, González PS, Agostini E. Proteomic analysis to unravel the biochemical mechanisms triggered by Bacillus toyonensis SFC 500-1E under chromium(VI) and phenol stress. Biometals 2023; 36:1081-1108. [PMID: 37209221 DOI: 10.1007/s10534-023-00506-9] [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: 01/17/2023] [Accepted: 04/24/2023] [Indexed: 05/22/2023]
Abstract
Bacillus toyonensis SFC 500-1E is a member of the consortium SFC 500-1 able to remove Cr(VI) and simultaneously tolerate high phenol concentrations. In order to elucidate mechanisms utilized by this strain during the bioremediation process, the differential expression pattern of proteins was analyzed when it grew with or without Cr(VI) (10 mg/L) and Cr(VI) + phenol (10 and 300 mg/L), through two complementary proteomic approaches: gel-based (Gel-LC) and gel-free (shotgun) nanoUHPLC-ESI-MS/MS. A total of 400 differentially expressed proteins were identified, out of which 152 proteins were down-regulated under Cr(VI) and 205 up-regulated in the presence of Cr(VI) + phenol, suggesting the extra effort made by the strain to adapt itself and keep growing when phenol was also added. The major metabolic pathways affected include carbohydrate and energetic metabolism, followed by lipid and amino acid metabolism. Particularly interesting were also ABC transporters and the iron-siderophore transporter as well as transcriptional regulators that can bind metals. Stress-associated global response involving the expression of thioredoxins, SOS response, and chaperones appears to be crucial for the survival of this strain under treatment with both contaminants. This research not only provided a deeper understanding of B. toyonensis SFC 500-1E metabolic role in Cr(VI) and phenol bioremediation process but also allowed us to complete an overview of the consortium SFC 500-1 behavior. This may contribute to an improvement in its use as a bioremediation strategy and also provides a baseline for further research.
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Affiliation(s)
- Marilina Fernandez
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto (UNRC), Ruta 36 Km 601, CP 5800, Río Cuarto, Córdoba, Argentina.
- CONICET, Instituto de Biotecnología Ambiental y Salud (INBIAS), Río Cuarto, Córdoba, Argentina.
| | - Eduardo A Callegari
- Division of Basic Biomedical Sciences Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | - María D Paez
- Division of Basic Biomedical Sciences Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | - Paola S González
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto (UNRC), Ruta 36 Km 601, CP 5800, Río Cuarto, Córdoba, Argentina
- CONICET, Instituto de Biotecnología Ambiental y Salud (INBIAS), Río Cuarto, Córdoba, Argentina
| | - Elizabeth Agostini
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto (UNRC), Ruta 36 Km 601, CP 5800, Río Cuarto, Córdoba, Argentina
- CONICET, Instituto de Biotecnología Ambiental y Salud (INBIAS), Río Cuarto, Córdoba, Argentina
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3
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MacKenzie TMG, Cisneros R, Maynard RD, Snyder MP. Reverse-ChIP Techniques for Identifying Locus-Specific Proteomes: A Key Tool in Unlocking the Cancer Regulome. Cells 2023; 12:1860. [PMID: 37508524 PMCID: PMC10377898 DOI: 10.3390/cells12141860] [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: 05/29/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
A phenotypic hallmark of cancer is aberrant transcriptional regulation. Transcriptional regulation is controlled by a complicated array of molecular factors, including the presence of transcription factors, the deposition of histone post-translational modifications, and long-range DNA interactions. Determining the molecular identity and function of these various factors is necessary to understand specific aspects of cancer biology and reveal potential therapeutic targets. Regulation of the genome by specific factors is typically studied using chromatin immunoprecipitation followed by sequencing (ChIP-Seq) that identifies genome-wide binding interactions through the use of factor-specific antibodies. A long-standing goal in many laboratories has been the development of a 'reverse-ChIP' approach to identify unknown binding partners at loci of interest. A variety of strategies have been employed to enable the selective biochemical purification of sequence-defined chromatin regions, including single-copy loci, and the subsequent analytical detection of associated proteins. This review covers mass spectrometry techniques that enable quantitative proteomics before providing a survey of approaches toward the development of strategies for the purification of sequence-specific chromatin as a 'reverse-ChIP' technique. A fully realized reverse-ChIP technique holds great potential for identifying cancer-specific targets and the development of personalized therapeutic regimens.
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Affiliation(s)
| | - Rocío Cisneros
- Sarafan ChEM-H/IMA Postbaccalaureate Fellow in Target Discovery, Stanford University, Stanford, CA 94305, USA
| | - Rajan D Maynard
- Genetics Department, Stanford University, Stanford, CA 94305, USA
| | - Michael P Snyder
- Genetics Department, Stanford University, Stanford, CA 94305, USA
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4
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Pakharukova MY, Savina E, Ponomarev DV, Gubanova NV, Zaparina O, Zakirova EG, Cheng G, Tikhonova OV, Mordvinov VA. Proteomic characterization of Opisthorchis felineus exosome-like vesicles and their uptake by human cholangiocytes. J Proteomics 2023; 283-284:104927. [PMID: 37225040 DOI: 10.1016/j.jprot.2023.104927] [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: 01/24/2023] [Revised: 03/18/2023] [Accepted: 05/03/2023] [Indexed: 05/26/2023]
Abstract
The epidemiologically important food-borne trematode Opisthorchis felineus infests the liver biliary tract of fish-eating mammals and causes disorders, including bile duct neoplasia. Many parasitic species release extracellular vesicles (EVs) that mediate host-parasite interaction. Currently, there is no information on O. felineus EVs. Using gel electrophoresis followed by liquid chromatography coupled with tandem mass spectrometry, we aimed to characterize the proteome of EVs released by the adult O. felineus liver fluke. Differential abundance of proteins between whole adult worms and EVs was assessed by semiquantitative iBAQ (intensity-based absolute quantification). Imaging, flow cytometry, inhibitor assays, and colocalization assays were performed to monitor the uptake of the EVs by H69 human cholangiocytes. The proteomic analysis reliably identified 168 proteins (at least two peptides matched a protein). Among major proteins of EVs were ferritin, tetraspanin CD63, helminth defense molecule 1, globin 3, saposin B type domain-containing protein, 60S ribosomal protein, glutathione S-transferase GST28, tubulin, and thioredoxin peroxidase. Moreover, as compared to the whole adult worm, EVs proved to be enriched with tetraspanin CD63, saposin B, helminth defense molecule 1, and Golgi-associated plant pathogenesis-related protein 1 (GAPR1). We showed that EVs are internalized by human H69 cholangiocytes via clathrin-dependent endocytosis, whereas phagocytosis and caveolin-dependent endocytosis do not play a substantial role in this process. Our study describes for the first time proteomes and differential abundance of proteins in whole adult O. felineus worms and EVs released by this food-borne trematode. Studies elucidating the regulatory role of individual components of EVs of liver flukes should be continued to determine which components of EV cargo play the most important part in the pathogenesis of fluke infection and in a closely linked pathology: bile duct neoplasia. SIGNIFICANCE: The food-borne trematode Opisthorchis felineus is a pathogen that causes hepatobiliary disorders in humans and animals. Our study describes for the first time the release of EVs by the liver fluke O. felineus, their microscopic and proteomic characterization, and internalization pathways by human cholangiocytes. Differential abundance of proteins between whole adult worms and EVs was assessed. EVs are enriched with canonical EV markers as well as parasite specific proteins, i.e. tetraspanin CD63, saposin B, helminth defense molecule 1, and others. Our findings will form the basis of the search for potential immunomodulatory candidates with therapeutic potential in the context of inflammatory diseases, as well as novel vaccine candidates.
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Affiliation(s)
- Maria Y Pakharukova
- Institute of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Akad. Lavrentiev Ave., Novosibirsk 630090, Russia; Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Str., Novosibirsk 630090, Russia.
| | - Ekaterina Savina
- Institute of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Akad. Lavrentiev Ave., Novosibirsk 630090, Russia
| | - Dmitry V Ponomarev
- Institute of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Akad. Lavrentiev Ave., Novosibirsk 630090, Russia
| | - Natalya V Gubanova
- Institute of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Akad. Lavrentiev Ave., Novosibirsk 630090, Russia
| | - Oxana Zaparina
- Institute of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Akad. Lavrentiev Ave., Novosibirsk 630090, Russia
| | - Elvira G Zakirova
- Institute of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Akad. Lavrentiev Ave., Novosibirsk 630090, Russia; Department of Genetic Technologies, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Guofeng Cheng
- Shanghai Tenth People's Hospital, Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, 301 Middle Yanchang Road, Shanghai 200072, China
| | - Olga V Tikhonova
- Institute of Biomedical Chemistry, 10 Pogodinskaya Str., 119121 Moscow, Russia
| | - Viatcheslav A Mordvinov
- Institute of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Akad. Lavrentiev Ave., Novosibirsk 630090, Russia
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5
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Woodland B, Necakov A, Coorssen JR. Optimized Proteome Reduction for Integrative Top–Down Proteomics. Proteomes 2023; 11:proteomes11010010. [PMID: 36976889 PMCID: PMC10059017 DOI: 10.3390/proteomes11010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/02/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Integrative top–down proteomics is an analytical approach that fully addresses the breadth and complexity needed for effective and routine assessment of proteomes. Nonetheless, any such assessments also require a rigorous review of methodology to ensure the deepest possible quantitative proteome analyses. Here, we establish an optimized general protocol for proteome extracts to improve the reduction of proteoforms and, thus, resolution in 2DE. Dithiothreitol (DTT), tributylphosphine (TBP), and 2-hydroxyethyldisulfide (HED), combined and alone, were tested in one-dimensional SDS-PAGE (1DE), prior to implementation into a full 2DE protocol. Prior to sample rehydration, reduction with 100 mM DTT + 5 mM TBP yielded increased spot counts, total signal, and spot circularity (i.e., decreased streaking) compared to other conditions and reduction protocols reported in the literature. The data indicate that many widely implemented reduction protocols are significantly ‘under-powered’ in terms of proteoform reduction and thus, limit the quality and depth of routine top–down proteomic analyses.
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Affiliation(s)
- Breyer Woodland
- Department of Biological Sciences, Faculty of Mathematics and Science, Brock University, St. Catharines, ON L2S 3A1, Canada
| | - Aleksandar Necakov
- Department of Biological Sciences, Faculty of Mathematics and Science, Brock University, St. Catharines, ON L2S 3A1, Canada
| | - Jens R. Coorssen
- Department of Biological Sciences, Faculty of Mathematics and Science, Brock University, St. Catharines, ON L2S 3A1, Canada
- Ronin Institute, Montclair, NJ 07043, USA
- Correspondence:
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6
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Mylonas R, Potts A, Waridel P, Barblan J, Conde Rubio MDC, Widmann C, Quadroni M. A Database of Accurate Electrophoretic Migration Patterns for Human Proteins. J Mol Biol 2023; 435:167933. [PMID: 36581244 DOI: 10.1016/j.jmb.2022.167933] [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: 10/13/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 12/27/2022]
Abstract
Native molecular weight (MW) is one of the defining features of proteins. Denaturing gel electrophoresis (SDS-PAGE) is a very popular technique for separating proteins and determining their MW. Coupled with antibody-based detection, SDS-PAGE is widely applied for protein identification and quantitation. Yet, electrophoresis is poorly reproducible and the MWs obtained are often inaccurate. This hampers antibody validation and negatively impacts the reliability of western blot data, resulting worldwide in a considerable waste of reagents and labour. We argue that, to alleviate these problems there is a need to establish a database of reference MWs measured by SDS-PAGE. Using mass spectrometry as an orthogonal detection method, we acquired electrophoretic migration patterns for approximately 10'000 human proteins in five commonly used cell lines. We applied a robust internal calibration of migration to determine accurate and reproducible molecular weights. This in turn allows merging replicates to increase accuracy, but also enables comparing different cell lines. Mining of the data obtained highlights structural factors that affect migration of distinct classes of proteins. When combined with peptide coverage, the data produced recapitulates known post-translational modifications and differential splicing and can be used to formulate hypotheses on new or poorly known processing events. The full information is freely accessible as a web resource through a user friendly graphical interface (https://pumba.dcsr.unil.ch/). We anticipate that this database will be useful to investigators worldwide for troubleshooting western blot experiments, but could also contribute to the characterization of human proteoforms.
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Affiliation(s)
- Roman Mylonas
- Protein Analysis Facility, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Alexandra Potts
- Protein Analysis Facility, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Patrice Waridel
- Protein Analysis Facility, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Jachen Barblan
- Protein Analysis Facility, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Maria Del Carmen Conde Rubio
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Christian Widmann
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Manfredo Quadroni
- Protein Analysis Facility, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
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7
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Genome-wide siRNA screens identify RBBP9 function as a potential target in Fanconi anaemia-deficient head-and-neck squamous cell carcinoma. Commun Biol 2023; 6:37. [PMID: 36639418 PMCID: PMC9839743 DOI: 10.1038/s42003-022-04389-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/19/2022] [Indexed: 01/15/2023] Open
Abstract
Fanconi anaemia (FA) is a rare chromosomal-instability syndrome caused by mutations of any of the 22 known FA DNA-repair genes. FA individuals have an increased risk of head-and-neck squamous-cell-carcinomas (HNSCC), often fatal. Systemic intolerance to standard cisplatin-based protocols due to somatic-cell hypersensitivity underscores the urgent need to develop novel therapies. Here, we performed unbiased siRNA screens to unveil genetic interactions synthetic-lethal with FA-pathway deficiency in FA-patient HNSCC cell lines. We identified based on differential-lethality scores between FA-deficient and FA-proficient cells, next to common-essential genes such as PSMC1, PSMB2, and LAMTOR2, the otherwise non-essential RBBP9 gene. Accordingly, low dose of the FDA-approved RBBP9-targeting drug Emetine kills FA-HNSCC. Importantly both RBBP9-silencing as well as Emetine spared non-tumour FA cells. This study provides a minable genome-wide analyses of vulnerabilities to address treatment challenges in FA-HNSCC. Our investigation divulges a DNA-cross-link-repair independent lead, RBBP9, for targeted treatment of FA-HNSCCs without systemic toxicity.
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8
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Di Stefano LH, Saba LJ, Oghbaie M, Jiang H, McKerrow W, Benitez-Guijarro M, Taylor MS, LaCava J. Affinity-Based Interactome Analysis of Endogenous LINE-1 Macromolecules. Methods Mol Biol 2023; 2607:215-256. [PMID: 36449166 DOI: 10.1007/978-1-0716-2883-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
During their proliferation and the host's concomitant attempts to suppress it, LINE-1 (L1) retrotransposons give rise to a collection of heterogeneous ribonucleoproteins (RNPs); their protein and RNA compositions remain poorly defined. The constituents of L1-associated macromolecules can differ depending on numerous factors, including, for example, position within the L1 life cycle, whether the macromolecule is productive or under suppression, and the cell type within which the proliferation is occurring. This chapter describes techniques that aid the capture and characterization of protein and RNA components of L1 macromolecules from tissues that natively express them. The protocols described have been applied to embryonal carcinoma cell lines that are popular model systems for L1 molecular biology (e.g., N2102Ep, NTERA-2, and PA-1 cells), as well as colorectal cancer tissues. N2102Ep cells are given as the use case for this chapter; the protocols should be applicable to essentially any tissue exhibiting endogenous L1 expression with minor modifications.
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9
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González-Gamboa I, Caparco AA, McCaskill JM, Steinmetz NF. Bioconjugation Strategies for Tobacco Mild Green Mosaic Virus. Chembiochem 2022; 23:e202200323. [PMID: 35835718 PMCID: PMC9624232 DOI: 10.1002/cbic.202200323] [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: 06/07/2022] [Revised: 07/03/2022] [Indexed: 11/06/2022]
Abstract
Tobacco mild green mosaic virus (TMGMV) is a plant virus closely related to Tobacco mosaic virus (TMV), sharing many of its structural and chemical features. These rod-shaped viruses, comprised of 2130 identical coat protein subunits, have been utilized as nanotechnological platforms for a myriad of applications, ranging from drug delivery to precision agriculture. This versatility for functionalization is due to their chemically active external and internal surfaces. While both viruses are similar, they do exhibit some key differences in their surface chemistry, suggesting the reactive residue distribution on TMGMV should not overlap with TMV. In this work, we focused on the establishment and refinement of chemical bioconjugation strategies to load molecules into or onto TMGMV for targeted delivery. A combination of NHS, EDC, and diazo coupling reactions in combination with click chemistry were used to modify the N-terminus, glutamic/aspartic acid residues, and tyrosines in TMGMV. We report loading with over 600 moieties per TMGMV via diazo-coupling, which is a >3-fold increase compared to previous studies. We also report that cargo can be loaded to the solvent-exposed N-terminus and carboxylates on the exterior/interior surfaces. Mass spectrometry revealed the most reactive sites to be Y12 and Y72, both tyrosine side chains are located on the exterior surface. For the carboxylates, interior E106 (66.53 %) was the most reactive for EDC-propargylamine coupled reactions, with the exterior E145 accounting for >15 % reactivity, overturning previous assumptions that only interior glutamic acid residues are accessible. A deeper understanding of the chemical properties of TMGMV further enables its functionalization and use as a multifunctional nanocarrier platform for applications in medicine and precision farming.
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Affiliation(s)
- Ivonne González-Gamboa
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Adam A Caparco
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Justin M McCaskill
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Nicole F Steinmetz
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
- Department of Radiology, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
- Center for Nano-ImmunoEngineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
- Institute for Materials Discovery and Design, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
- Moores Cancer Center, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
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10
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Chen C, Wen M, Jin Y. 1DE-MS Profiling for Proteoform-Correlated Proteomic Analysis, by Combining SDS-PAGE, Whole-Gel Slicing, Quantitative LC-MS/MS, and Reconstruction of Gel Distributions of Several Thousands of Proteins. J Proteome Res 2022; 21:2311-2330. [PMID: 36018058 DOI: 10.1021/acs.jproteome.2c00180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
SDS-PAGE has often been used in proteomic analysis, but generally for sample prefractionation although the technique separates proteins by molecular masses (Mws) and the information would contribute to proteoform-level analysis. Here, we report a method that combines SDS-PAGE, whole-gel slicing, and quantitative LC-MS/MS for establishing gel distributions of several thousand proteins in a proteome. A previously obtained data set on rat cerebral cortex with cerebral ischemia-reperfusion injury1 was analyzed, and the gel distributions of 5906 proteins were reconstructed. These distributions, referred to as 1DE-MS profiles, revealed that about 30% of the proteins had more than one proteoform detected in the gels. The profiles were categorized into six types by distribution (narrow, dispersed, or broad) and relative deviations between the abundance-peak apparent Mws and calculated Mws. Only 56% of the proteins showed narrow distributions and matched Mws, while the others had rather complex profiles. Bioinformatic analysis on example profiles showed the resolved proteoforms involved alternative splicing, proteolytic processing, glycosylation and ubiquitination, fragmentation, and probably transmembrane structures. Profile-based differential analysis revealed that many of the disease-caused changes were proteoform dependent. This work provided a proteome-scale view of protein distributions in SDS-PAGE gels, and the method would be useful to obtain proteoform-correlated information for in-depth proteomics.
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Affiliation(s)
- Changming Chen
- Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, P. R. China
| | - Meiling Wen
- Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, P. R. China
| | - Ya Jin
- Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, P. R. China
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11
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Applications of Tandem Mass Spectrometry (MS/MS) in Protein Analysis for Biomedical Research. Molecules 2022; 27:molecules27082411. [PMID: 35458608 PMCID: PMC9031286 DOI: 10.3390/molecules27082411] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 01/27/2023] Open
Abstract
Mass Spectrometry (MS) allows the analysis of proteins and peptides through a variety of methods, such as Electrospray Ionization-Mass Spectrometry (ESI-MS) or Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry (MALDI-MS). These methods allow identification of the mass of a protein or a peptide as intact molecules or the identification of a protein through peptide-mass fingerprinting generated upon enzymatic digestion. Tandem mass spectrometry (MS/MS) allows the fragmentation of proteins and peptides to determine the amino acid sequence of proteins (top-down and middle-down proteomics) and peptides (bottom-up proteomics). Furthermore, tandem mass spectrometry also allows the identification of post-translational modifications (PTMs) of proteins and peptides. Here, we discuss the application of MS/MS in biomedical research, indicating specific examples for the identification of proteins or peptides and their PTMs as relevant biomarkers for diagnostic and therapy.
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12
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Mumtaz M, Bijnsdorp IV, Böttger F, Piersma SR, Pham TV, Mumtaz S, Brakenhoff RH, Akhtar MW, Jimenez CR. Secreted protein markers in oral squamous cell carcinoma (OSCC). Clin Proteomics 2022; 19:4. [PMID: 35130834 PMCID: PMC8903575 DOI: 10.1186/s12014-022-09341-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/12/2022] [Indexed: 12/24/2022] Open
Abstract
Background Oral squamous cell carcinoma (OSCC) is a main cause of oral cancer mortality and morbidity in central south Asia. To improve the clinical outcome of OSCC patients, detection markers are needed, which are preferably non-invasive and thus independent of a tissue biopsy. Methods In the present study, we aimed to identify robust candidate protein biomarkers for non-invasive OSCC diagnosis. To this end, we measured the global protein profiles of OSCC tissue lysates to matched normal adjacent mucosa samples (n = 14) and the secretomes of nine HNSCC cell lines using LC–MS/MS-based proteomics. Results A total of 5123 tissue proteins were identified, of which 205 were robustly up- regulated (p-value < 0.01, fold change > + 2) in OSCC-tissues compared to normal adjacent tissues. The biological process “Secretion” was highly enriched in this set of proteins. Other upregulated biological pathways included “Unfolded Protein Response”, “Spliceosomal complex assembly”, “Protein localization to endosome” and “Interferon Gamma Response”. Transcription factor analysis implicated Creb3L1, ESRRA, YY, ELF2, STAT1 and XBP as potential regulators. Of the 205 upregulated tissue proteins, 132 were identified in the cancer cell line secretomes, underscoring their potential use as non-invasive biofluid markers. To further prioritize our candidate markers for non-invasive OSCC detection, we integrated our data with public biofluid datasets including OSCC saliva, yielding 25 candidate markers for further study. Conclusions We identified several key proteins and processes that are associated with OSCC tissues, underscoring the importance of altered secretion. Cancer-associated OSCC secretome proteins present in saliva have potential to be used as novel non-invasive biomarkers for the diagnosis of OSCC. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12014-022-09341-5.
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Affiliation(s)
- Madiha Mumtaz
- School of Biological Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Irene V Bijnsdorp
- Department of Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam UMC, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands.,Department of Urology, Cancer Center Amsterdam, Amsterdam UMC, de Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Franziska Böttger
- Department of Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam UMC, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam UMC, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam UMC, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | | | - Ruud H Brakenhoff
- Department of Otolaryngology/Head and Neck Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - M Waheed Akhtar
- School of Biological Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Connie R Jimenez
- Department of Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam UMC, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands.
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13
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Paez MD, Callegari EA. Proteomics Analysis of the Estrogen Effects in the Rat Uterus Using Gel-LC and Tandem Mass Spectrometry Approaches. Methods Mol Biol 2022; 2418:289-311. [PMID: 35119672 DOI: 10.1007/978-1-0716-1920-9_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Proteomics-based bottoms-up, at a big scale applied to the protein identification and relative quantification present in complex mixtures (cell lysates, tissues, biological fluids, secretome, etc.) is a useful strategy to identify proteins and analyze their changes. Samples processed through a gel-free approach provide a simple method for protein separation and profile comparison of different conditions, such as using fewer steps in the protocol, reducing excessive sample handling, and covering an extended range of molecular weights and isoelectric points. However, it presents a great limitation related to the management of large dynamic ranges of proteins. There are numerous protocols that allow handling the problem or limitations generated by a high dynamic range of the proteins present in the sample. The Gel-LC technique is a complementary alternative of the gel-free approach available to solve the issue of protein samples with a high dynamic range. The different steps of the protocol involve sample processing through Gel-LC (1D-SDS-PAGE) prior to digestion, 1D-nanoUHPLC coupled to high-resolution/mass accuracy tandem mass spectrometry analysis (1D-nanoUHPLC-HR/MA-MS /MS analysis) and afterward, the protein identification and relative quantification analysis using bioinformatics tools for the data conversion, organization, and interpretation.
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Affiliation(s)
- Maria D Paez
- Division of Basic Biomedical Sciences, Sanford School of Medicine of the University of South Dakota, Vermillion, SD, USA.
| | - Eduardo A Callegari
- Division of Basic Biomedical Sciences, Sanford School of Medicine of the University of South Dakota, Vermillion, SD, USA.
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14
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Montana V, Flint D, Waagepetersen HS, Schousboe A, Parpura V. Two Metabolic Fuels, Glucose and Lactate, Differentially Modulate Exocytotic Glutamate Release from Cultured Astrocytes. Neurochem Res 2021; 46:2551-2579. [PMID: 34057673 PMCID: PMC9015689 DOI: 10.1007/s11064-021-03340-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/06/2021] [Accepted: 05/10/2021] [Indexed: 12/26/2022]
Abstract
Astrocytes have a prominent role in metabolic homeostasis of the brain and can signal to adjacent neurons by releasing glutamate via a process of regulated exocytosis. Astrocytes synthesize glutamate de novo owing to the pyruvate entry to the citric/tricarboxylic acid cycle via pyruvate carboxylase, an astrocyte specific enzyme. Pyruvate can be sourced from two metabolic fuels, glucose and lactate. Thus, we investigated the role of these energy/carbon sources in exocytotic glutamate release from astrocytes. Purified astrocyte cultures were acutely incubated (1 h) in glucose and/or lactate-containing media. Astrocytes were mechanically stimulated, a procedure known to increase intracellular Ca2+ levels and cause exocytotic glutamate release, the dynamics of which were monitored using single cell fluorescence microscopy. Our data indicate that glucose, either taken-up from the extracellular space or mobilized from the intracellular glycogen storage, sustained glutamate release, while the availability of lactate significantly reduced the release of glutamate from astrocytes. Based on further pharmacological manipulation during imaging along with tandem mass spectrometry (proteomics) analysis, lactate alone, but not in the hybrid fuel, caused metabolic changes consistent with an increased synthesis of fatty acids. Proteomics analysis further unveiled complex changes in protein profiles, which were condition-dependent and generally included changes in levels of cytoskeletal proteins, proteins of secretory organelle/vesicle traffic and recycling at the plasma membrane in aglycemic, lactate or hybrid-fueled astrocytes. These findings support the notion that the availability of energy sources and metabolic milieu play a significant role in gliotransmission.
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Affiliation(s)
- Vedrana Montana
- Department of Neurobiology, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
| | - Daniel Flint
- Luxumbra Strategic Research, LLC, Arlington, VA, USA
| | - Helle S Waagepetersen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Arne Schousboe
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vladimir Parpura
- Department of Neurobiology, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
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15
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Ushakova NA, Brodsky ES, Tikhonova OV, Dontsov AE, Marsova MV, Shelepchikov AA, Bastrakov AI. Novel Extract from Beetle Ulomoides dermestoides: A Study of Composition and Antioxidant Activity. Antioxidants (Basel) 2021; 10:antiox10071055. [PMID: 34208791 PMCID: PMC8300742 DOI: 10.3390/antiox10071055] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/19/2021] [Accepted: 06/25/2021] [Indexed: 01/05/2023] Open
Abstract
A biologically active extract from the darkling beetle Ulomoides dermestoides was obtained using the electro-pulse plasma dynamic extraction method. The beetle water extract contained a complex of antioxidant substances such as antioxidant enzymes and nonprotein antioxidants, as well as a complex of heat shock antistress proteins. This determines the rather high antioxidant activity of the aqueous extract of the beetle, i.e., 1 mg of dry matter/mL of the extract has an equivalent antioxidant activity to 0.2 mM Trolox (a water-soluble analog of vitamin E). It was shown that the beetle extract can lead to a 25-30% increase in the average lifespan of nematode Caenorhabditiselegans, under normal conditions, and a 12-17% increase under conditions of oxidative stress (with paraquat), and significantly inhibits the fructosylation reaction of serum albumin. Therefore, the beetle aqueous extract shows promise as a biologically active complex exhibiting antioxidant activity.
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Affiliation(s)
- Nina A. Ushakova
- A.N. Severtsov Institute of Ecology and Evolution RAS, Leninsky Prospect, 33, 119071 Moscow, Russia; (N.A.U.); (E.S.B.); (A.A.S.); (A.I.B.)
| | - Efim S. Brodsky
- A.N. Severtsov Institute of Ecology and Evolution RAS, Leninsky Prospect, 33, 119071 Moscow, Russia; (N.A.U.); (E.S.B.); (A.A.S.); (A.I.B.)
| | - Olga V. Tikhonova
- Institute of Biomedical Chemistry (IBMC), Pogodinskaya Str., 10, 119121 Moscow, Russia;
| | - Alexander E. Dontsov
- N.M. Emanuel Institute of Biochemical Physics, RAS, Kosygina Str., 4, 119334 Moscow, Russia
- Correspondence:
| | - Maria V. Marsova
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina Str., 3, 119991 Moscow, Russia;
| | - Andrey A. Shelepchikov
- A.N. Severtsov Institute of Ecology and Evolution RAS, Leninsky Prospect, 33, 119071 Moscow, Russia; (N.A.U.); (E.S.B.); (A.A.S.); (A.I.B.)
| | - Alexander I. Bastrakov
- A.N. Severtsov Institute of Ecology and Evolution RAS, Leninsky Prospect, 33, 119071 Moscow, Russia; (N.A.U.); (E.S.B.); (A.A.S.); (A.I.B.)
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16
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Le Large TYS, Bijlsma MF, El Hassouni B, Mantini G, Lagerweij T, Henneman AA, Funel N, Kok B, Pham TV, de Haas R, Morelli L, Knol JC, Piersma SR, Kazemier G, van Laarhoven HWM, Giovannetti E, Jimenez CR. Focal adhesion kinase inhibition synergizes with nab-paclitaxel to target pancreatic ductal adenocarcinoma. J Exp Clin Cancer Res 2021; 40:91. [PMID: 33750427 PMCID: PMC7941981 DOI: 10.1186/s13046-021-01892-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/24/2021] [Indexed: 02/08/2023] Open
Abstract
Background Pancreatic ductal adenocarcinoma (PDAC) is a very lethal disease, with minimal therapeutic options. Aberrant tyrosine kinase activity influences tumor growth and is regulated by phosphorylation. We investigated phosphorylated kinases as target in PDAC. Methods Mass spectrometry-based phosphotyrosine proteomic analysis on PDAC cell lines was used to evaluate active kinases. Pathway analysis and inferred kinase activity analysis was performed to identify novel targets. Subsequently, we investigated targeting of focal adhesion kinase (FAK) in vitro with drug perturbations in combination with chemotherapeutics used against PDAC. Tyrosine phosphoproteomics upon treatment was performed to evaluate signaling. An orthotopic model of PDAC was used to evaluate the combination of defactinib with nab-paclitaxel. Results PDAC cell lines portrayed high activity of multiple receptor tyrosine kinases to various degree. The non-receptor kinase, FAK, was identified in all cell lines by our phosphotyrosine proteomic screen and pathway analysis. Targeting of this kinase with defactinib validated reduced phosphorylation profiles. Additionally, FAK inhibition had anti-proliferative and anti-migratory effects. Combination with (nab-)paclitaxel had a synergistic effect on cell proliferation in vitro and reduced tumor growth in vivo. Conclusions Our study shows high phosphorylation of several oncogenic receptor tyrosine kinases in PDAC cells and validated FAK inhibition as potential synergistic target with Nab-paclitaxel against this devastating disease. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-01892-z.
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Affiliation(s)
- T Y S Le Large
- Department of Surgery, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University Amsterdam, Amsterdam, The Netherlands.,Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University, De Boelelaan 1117, 1081, HV, Amsterdam, The Netherlands.,Laboratory for Experimental Oncology and Radiobiology, Cancer Center Amsterdam, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, the Netherlands.,OncoProteomics Laboratory, Department of Medical Oncology, Cancer, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University, De Boelelaan 1117, 1081, HV, Amsterdam, The Netherlands
| | - M F Bijlsma
- Laboratory for Experimental Oncology and Radiobiology, Cancer Center Amsterdam, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, the Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - B El Hassouni
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University, De Boelelaan 1117, 1081, HV, Amsterdam, The Netherlands
| | - G Mantini
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University, De Boelelaan 1117, 1081, HV, Amsterdam, The Netherlands.,OncoProteomics Laboratory, Department of Medical Oncology, Cancer, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University, De Boelelaan 1117, 1081, HV, Amsterdam, The Netherlands.,Cancer Pharmacology Lab, AIRC-Start-Up, Fondazione Pisana per la Scienza, Pisa, Italy
| | - T Lagerweij
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University, De Boelelaan 1117, 1081, HV, Amsterdam, The Netherlands.,Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University Amsterdam, Amsterdam, The Netherlands
| | - A A Henneman
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University, De Boelelaan 1117, 1081, HV, Amsterdam, The Netherlands
| | - N Funel
- Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - B Kok
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University, De Boelelaan 1117, 1081, HV, Amsterdam, The Netherlands
| | - T V Pham
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University, De Boelelaan 1117, 1081, HV, Amsterdam, The Netherlands
| | - R de Haas
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University, De Boelelaan 1117, 1081, HV, Amsterdam, The Netherlands
| | - L Morelli
- Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - J C Knol
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University, De Boelelaan 1117, 1081, HV, Amsterdam, The Netherlands
| | - S R Piersma
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University, De Boelelaan 1117, 1081, HV, Amsterdam, The Netherlands
| | - G Kazemier
- Department of Surgery, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University Amsterdam, Amsterdam, The Netherlands
| | - H W M van Laarhoven
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University, De Boelelaan 1117, 1081, HV, Amsterdam, The Netherlands.,Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - E Giovannetti
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University, De Boelelaan 1117, 1081, HV, Amsterdam, The Netherlands. .,Cancer Pharmacology Lab, AIRC-Start-Up, Fondazione Pisana per la Scienza, Pisa, Italy.
| | - C R Jimenez
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University, De Boelelaan 1117, 1081, HV, Amsterdam, The Netherlands.
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17
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Visscher DO, Lee H, van Zuijlen PPM, Helder MN, Atala A, Yoo JJ, Lee SJ. A photo-crosslinkable cartilage-derived extracellular matrix bioink for auricular cartilage tissue engineering. Acta Biomater 2021; 121:193-203. [PMID: 33227486 PMCID: PMC7855948 DOI: 10.1016/j.actbio.2020.11.029] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/12/2020] [Accepted: 11/17/2020] [Indexed: 12/15/2022]
Abstract
Three-dimensional (3D) bioprinting of patient-specific auricular cartilage constructs could aid in the reconstruction process of traumatically injured or congenitally deformed ear cartilage. To achieve this, a hydrogel-based bioink is required that recapitulates the complex cartilage microenvironment. Tissue-derived decellularized extracellular matrix (dECM)-based hydrogels have been used as bioinks for cell-based 3D bioprinting because they contain tissue-specific ECM components that play a vital role in cell adhesion, growth, and differentiation. In this study, porcine auricular cartilage tissues were isolated and decellularized, and the decellularized cartilage tissues were characterized by histology, biochemical assay, and proteomics. This cartilage-derived dECM (cdECM) was subsequently processed into a photo-crosslinkable hydrogel using methacrylation (cdECMMA) and mixed with chondrocytes to create a printable bioink. The rheological properties, printability, and in vitro biological properties of the cdECMMA bioink were examined. The results showed cdECM was obtained with complete removal of cellular components while preserving major ECM proteins. After methacrylation, the cdECMMA bioinks were printed in anatomical ear shape and exhibited adequate mechanical properties and structural integrity. Specifically, auricular chondrocytes in the printed cdECMMA hydrogel constructs maintained their viability and proliferation capacity and eventually produced cartilage ECM components, including collagen and glycosaminoglycans (GAGs). The potential of cell-based bioprinting using this cartilage-specific dECMMA bioink is demonstrated as an alternative option for auricular cartilage reconstruction.
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Affiliation(s)
- Dafydd O Visscher
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA; Department of Plastic, Reconstructive, and Hand Surgery, Amsterdam UMC, Amsterdam 1081HV, the Netherlands
| | - Hyeongjin Lee
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - Paul P M van Zuijlen
- Department of Plastic, Reconstructive, and Hand Surgery, Amsterdam UMC, Amsterdam 1081HV, the Netherlands; Department of Plastic, Reconstructive, and Hand Surgery, Red Cross Hospital, Beverwijk 1942LE, the Netherlands
| | - Marco N Helder
- Department of Oral and Maxillofacial Surgery/Oral Pathology-3D Innovation Lab, Amsterdam UMC, Amsterdam 1081HV, the Netherlands
| | - Anthony Atala
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - James J Yoo
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - Sang Jin Lee
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA.
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18
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Glykofridis IE, Knol JC, Balk JA, Westland D, Pham TV, Piersma SR, Lougheed SM, Derakhshan S, Veen P, Rooimans MA, van Mil SE, Böttger F, Poddighe PJ, van de Beek I, Drost J, Zwartkruis FJ, de Menezes RX, Meijers-Heijboer HE, Houweling AC, Jimenez CR, Wolthuis RM. Loss of FLCN-FNIP1/2 induces a non-canonical interferon response in human renal tubular epithelial cells. eLife 2021; 10:61630. [PMID: 33459596 PMCID: PMC7899648 DOI: 10.7554/elife.61630] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/16/2021] [Indexed: 12/14/2022] Open
Abstract
Germline mutations in the Folliculin (FLCN) tumor suppressor gene cause Birt–Hogg–Dubé (BHD) syndrome, a rare autosomal dominant disorder predisposing carriers to kidney tumors. FLCN is a conserved, essential gene linked to diverse cellular processes but the mechanism by which FLCN prevents kidney cancer remains unknown. Here, we show that disrupting FLCN in human renal tubular epithelial cells (RPTEC/TERT1) activates TFE3, upregulating expression of its E-box targets, including RRAGD and GPNMB, without modifying mTORC1 activity. Surprisingly, the absence of FLCN or its binding partners FNIP1/FNIP2 induces interferon response genes independently of interferon. Mechanistically, FLCN loss promotes STAT2 recruitment to chromatin and slows cellular proliferation. Our integrated analysis identifies STAT1/2 signaling as a novel target of FLCN in renal cells and BHD tumors. STAT1/2 activation appears to counterbalance TFE3-directed hyper-proliferation and may influence immune responses. These findings shed light on unique roles of FLCN in human renal tumorigenesis and pinpoint candidate prognostic biomarkers.
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Affiliation(s)
- Iris E Glykofridis
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Jaco C Knol
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Jesper A Balk
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Denise Westland
- University Medical Center Utrecht, Center for Molecular Medicine, Molecular Cancer Research, Universiteitsweg, Utrecht, Netherlands
| | - Thang V Pham
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Sander R Piersma
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Sinéad M Lougheed
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Sepide Derakhshan
- Princess Máxima Center for Pediatric Oncology, Oncode Institute, Heidelberglaan, Utrecht, Netherlands
| | - Puck Veen
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Martin A Rooimans
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Saskia E van Mil
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Franziska Böttger
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Pino J Poddighe
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Amsterdam, Netherlands
| | - Irma van de Beek
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Amsterdam, Netherlands
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Oncode Institute, Heidelberglaan, Utrecht, Netherlands
| | - Fried Jt Zwartkruis
- University Medical Center Utrecht, Center for Molecular Medicine, Molecular Cancer Research, Universiteitsweg, Utrecht, Netherlands
| | | | - Hanne Ej Meijers-Heijboer
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Arjan C Houweling
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Amsterdam, Netherlands
| | - Connie R Jimenez
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Rob Mf Wolthuis
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Cancer Center Amsterdam, Amsterdam, Netherlands
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19
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Visscher DO, Lee H, van Zuijlen PPM, Helder MN, Atala A, Yoo JJ, Lee SJ. A photo-crosslinkable cartilage-derived extracellular matrix bioink for auricular cartilage tissue engineering. Acta Biomater 2020. [PMID: 33227486 DOI: 10.1016/j.actbio.2020.11.029.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Three-dimensional (3D) bioprinting of patient-specific auricular cartilage constructs could aid in the reconstruction process of traumatically injured or congenitally deformed ear cartilage. To achieve this, a hydrogel-based bioink is required that recapitulates the complex cartilage microenvironment. Tissue-derived decellularized extracellular matrix (dECM)-based hydrogels have been used as bioinks for cell-based 3D bioprinting because they contain tissue-specific ECM components that play a vital role in cell adhesion, growth, and differentiation. In this study, porcine auricular cartilage tissues were isolated and decellularized, and the decellularized cartilage tissues were characterized by histology, biochemical assay, and proteomics. This cartilage-derived dECM (cdECM) was subsequently processed into a photo-crosslinkable hydrogel using methacrylation (cdECMMA) and mixed with chondrocytes to create a printable bioink. The rheological properties, printability, and in vitro biological properties of the cdECMMA bioink were examined. The results showed cdECM was obtained with complete removal of cellular components while preserving major ECM proteins. After methacrylation, the cdECMMA bioinks were printed in anatomical ear shape and exhibited adequate mechanical properties and structural integrity. Specifically, auricular chondrocytes in the printed cdECMMA hydrogel constructs maintained their viability and proliferation capacity and eventually produced cartilage ECM components, including collagen and glycosaminoglycans (GAGs). The potential of cell-based bioprinting using this cartilage-specific dECMMA bioink is demonstrated as an alternative option for auricular cartilage reconstruction.
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Affiliation(s)
- Dafydd O Visscher
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA; Department of Plastic, Reconstructive, and Hand Surgery, Amsterdam UMC, Amsterdam 1081HV, the Netherlands
| | - Hyeongjin Lee
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - Paul P M van Zuijlen
- Department of Plastic, Reconstructive, and Hand Surgery, Amsterdam UMC, Amsterdam 1081HV, the Netherlands; Department of Plastic, Reconstructive, and Hand Surgery, Red Cross Hospital, Beverwijk 1942LE, the Netherlands
| | - Marco N Helder
- Department of Oral and Maxillofacial Surgery/Oral Pathology-3D Innovation Lab, Amsterdam UMC, Amsterdam 1081HV, the Netherlands
| | - Anthony Atala
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - James J Yoo
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - Sang Jin Lee
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA.
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20
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Le Large TY, Mantini G, Meijer LL, Pham TV, Funel N, van Grieken NC, Kok B, Knol J, van Laarhoven HW, Piersma SR, Jimenez CR, Kazemier G, Giovannetti E, Bijlsma MF. Microdissected pancreatic cancer proteomes reveal tumor heterogeneity and therapeutic targets. JCI Insight 2020; 5:138290. [PMID: 32634123 PMCID: PMC7455080 DOI: 10.1172/jci.insight.138290] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/24/2020] [Indexed: 12/12/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized by a relative paucity of cancer cells that are surrounded by an abundance of nontumor cells and extracellular matrix, known as stroma. The interaction between stroma and cancer cells contributes to poor outcome, but how proteins from these individual compartments drive aggressive tumor behavior is not known. Here, we report the proteomic analysis of laser-capture microdissected (LCM) PDAC samples. We isolated stroma, tumor, and bulk samples from a cohort with long- and short-term survivors. Compartment-specific proteins were measured by mass spectrometry, yielding what we believe to be the largest PDAC proteome landscape to date. These analyses revealed that, in bulk analysis, tumor-derived proteins were typically masked and that LCM was required to reveal biology and prognostic markers. We validated tumor CALB2 and stromal COL11A1 expression as compartment-specific prognostic markers. We identified and functionally addressed the contributions of the tumor cell receptor EPHA2 to tumor cell viability and motility, underscoring the value of compartment-specific protein analysis in PDAC.
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Affiliation(s)
- Tessa Y.S. Le Large
- Department of Surgery and
- Department of Medical Oncology, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
- Laboratory for Experimental Oncology and Radiobiology, Amsterdam University Medical Centers, University of Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
- OncoProteomics Laboratory, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Giulia Mantini
- Department of Medical Oncology, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
- OncoProteomics Laboratory, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
- Cancer Pharmacology Lab, Fondazione Pisana per la Scienza, Pisa, Italy
| | - Laura L. Meijer
- Department of Surgery and
- Department of Medical Oncology, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Thang V. Pham
- Department of Medical Oncology, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
- OncoProteomics Laboratory, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Niccola Funel
- Unit of Anatomic Pathology II, Azienda Ospedaliera Universitaria Pisana, Pisa, Italy
| | | | | | - Jaco Knol
- Department of Medical Oncology, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
- OncoProteomics Laboratory, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Hanneke W.M. van Laarhoven
- Department of Medical Oncology, Amsterdam University Medical Centers, University of Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Sander R. Piersma
- Department of Medical Oncology, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
- OncoProteomics Laboratory, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Connie R. Jimenez
- Department of Medical Oncology, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
- OncoProteomics Laboratory, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | | | - Elisa Giovannetti
- Department of Medical Oncology, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
- Cancer Pharmacology Lab, Fondazione Pisana per la Scienza, Pisa, Italy
| | - Maarten F. Bijlsma
- Laboratory for Experimental Oncology and Radiobiology, Amsterdam University Medical Centers, University of Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
- Oncode Institute, Amsterdam, Netherlands
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21
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van Steenoven I, Koel-Simmelink MJA, Vergouw LJM, Tijms BM, Piersma SR, Pham TV, Bridel C, Ferri GL, Cocco C, Noli B, Worley PF, Xiao MF, Xu D, Oeckl P, Otto M, van der Flier WM, de Jong FJ, Jimenez CR, Lemstra AW, Teunissen CE. Identification of novel cerebrospinal fluid biomarker candidates for dementia with Lewy bodies: a proteomic approach. Mol Neurodegener 2020; 15:36. [PMID: 32552841 PMCID: PMC7301448 DOI: 10.1186/s13024-020-00388-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 06/08/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Diagnosis of dementia with Lewy bodies (DLB) is challenging, largely due to a lack of diagnostic tools. Cerebrospinal fluid (CSF) biomarkers have been proven useful in Alzheimer's disease (AD) diagnosis. Here, we aimed to identify novel CSF biomarkers for DLB using a high-throughput proteomic approach. METHODS We applied liquid chromatography/tandem mass spectrometry with label-free quantification to identify biomarker candidates to individual CSF samples from a well-characterized cohort comprising patients with DLB (n = 20) and controls (n = 20). Validation was performed using (1) the identical proteomic workflow in an independent cohort (n = 30), (2) proteomic data from patients with related neurodegenerative diseases (n = 149) and (3) orthogonal techniques in an extended cohort consisting of DLB patients and controls (n = 76). Additionally, we utilized random forest analysis to identify the subset of candidate markers that best distinguished DLB from all other groups. RESULTS In total, we identified 1995 proteins. In the discovery cohort, 69 proteins were differentially expressed in DLB compared to controls (p < 0.05). Independent cohort replication confirmed VGF, SCG2, NPTX2, NPTXR, PDYN and PCSK1N as candidate biomarkers for DLB. The downregulation of the candidate biomarkers was somewhat more pronounced in DLB in comparison with related neurodegenerative diseases. Using random forest analysis, we identified a panel of VGF, SCG2 and PDYN to best differentiate between DLB and other clinical groups (accuracy: 0.82 (95%CI: 0.75-0.89)). Moreover, we confirmed the decrease of VGF and NPTX2 in DLB by ELISA and SRM methods. Low CSF levels of all biomarker candidates, except PCSK1N, were associated with more pronounced cognitive decline (0.37 < r < 0.56, all p < 0.01). CONCLUSION We identified and validated six novel CSF biomarkers for DLB. These biomarkers, particularly when used as a panel, show promise to improve diagnostic accuracy and strengthen the importance of synaptic dysfunction in the pathophysiology of DLB.
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Affiliation(s)
- Inger van Steenoven
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Marleen J. A. Koel-Simmelink
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Leonie J. M. Vergouw
- Alzheimer Center Erasmus MC, Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Betty M. Tijms
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Sander R. Piersma
- OncoProteomics Laboratory, Department of Medical Oncology, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Thang V. Pham
- OncoProteomics Laboratory, Department of Medical Oncology, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Claire Bridel
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Gian-Luca Ferri
- NEF-laboratory, Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Cristina Cocco
- NEF-laboratory, Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Barbara Noli
- NEF-laboratory, Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Paul F. Worley
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Mei-Fang Xiao
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Desheng Xu
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Patrick Oeckl
- Department of Neurology, Ulm University Hospital, Ulm, Germany
| | - Markus Otto
- Department of Neurology, Ulm University Hospital, Ulm, Germany
| | - Wiesje M. van der Flier
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
- Department of Epidemiology and Biostatistics, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Frank Jan de Jong
- Alzheimer Center Erasmus MC, Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Connie R. Jimenez
- OncoProteomics Laboratory, Department of Medical Oncology, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Afina W. Lemstra
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Charlotte E. Teunissen
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
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22
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Turaihi AH, Serné EH, Molthoff CFM, Koning JJ, Knol J, Niessen HW, Goumans MJTH, van Poelgeest EM, Yudkin JS, Smulders YM, Jimenez CR, van Hinsbergh VWM, Eringa EC. Perivascular Adipose Tissue Controls Insulin-Stimulated Perfusion, Mitochondrial Protein Expression, and Glucose Uptake in Muscle Through Adipomuscular Arterioles. Diabetes 2020; 69:603-613. [PMID: 32005705 DOI: 10.2337/db18-1066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/24/2020] [Indexed: 11/13/2022]
Abstract
Insulin-mediated microvascular recruitment (IMVR) regulates delivery of insulin and glucose to insulin-sensitive tissues. We have previously proposed that perivascular adipose tissue (PVAT) controls vascular function through outside-to-inside communication and through vessel-to-vessel, or "vasocrine," signaling. However, direct experimental evidence supporting a role of local PVAT in regulating IMVR and insulin sensitivity in vivo is lacking. Here, we studied muscles with and without PVAT in mice using combined contrast-enhanced ultrasonography and intravital microscopy to measure IMVR and gracilis artery diameter at baseline and during the hyperinsulinemic-euglycemic clamp. We show, using microsurgical removal of PVAT from the muscle microcirculation, that local PVAT depots regulate insulin-stimulated muscle perfusion and glucose uptake in vivo. We discovered direct microvascular connections between PVAT and the distal muscle microcirculation, or adipomuscular arterioles, the removal of which abolished IMVR. Local removal of intramuscular PVAT altered protein clusters in the connected muscle, including upregulation of a cluster featuring Hsp90ab1 and Hsp70 and downregulation of a cluster of mitochondrial protein components of complexes III, IV, and V. These data highlight the importance of PVAT in vascular and metabolic physiology and are likely relevant for obesity and diabetes.
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Affiliation(s)
- Alexander H Turaihi
- Department of Physiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Erik H Serné
- Department of Internal Medicine, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Carla F M Molthoff
- Department of Radiology and Nuclear Medicine, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Jasper J Koning
- Department of Molecular Cell Biology and Immunology, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Jaco Knol
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Hans W Niessen
- Department of Pathology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Marie Jose T H Goumans
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Erik M van Poelgeest
- Department of Physiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - John S Yudkin
- Institute of Cardiovascular Science, Division of Medicine, University College London, London, U.K
| | - Yvo M Smulders
- Department of Internal Medicine, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Connie R Jimenez
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Victor W M van Hinsbergh
- Department of Physiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Etto C Eringa
- Department of Physiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Center, Amsterdam, the Netherlands
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23
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Ndumiso M, Buchtová N, Husselmann L, Mohamed G, Klein A, Aucamp M, Canevet D, D'Souza S, Maphasa RE, Boury F, Dube A. Comparative whole corona fingerprinting and protein adsorption thermodynamics of PLGA and PCL nanoparticles in human serum. Colloids Surf B Biointerfaces 2020; 188:110816. [PMID: 31991290 PMCID: PMC7061085 DOI: 10.1016/j.colsurfb.2020.110816] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 12/24/2019] [Accepted: 01/20/2020] [Indexed: 12/31/2022]
Abstract
Nanoparticles (NPs) based on biocompatible and biodegradable polymers such as poly(lactic-co-glycolic acid) (PLGA) and polycaprolactone (PCL) represent effective systems for systemic drug delivery. Upon injection into the blood circuit, the NP surface is rapidly modified due to adsorption of proteins that form a 'protein corona' (PC). The PC plays an important role in cellular targeting, uptake and NP bio-distribution. Hence, the study of interactions between NPs and serum proteins appears as key for biomedical applications and safety of NPs. In the present work, we report on the comparative protein fluorescence quenching extent, thermodynamics of protein binding and identification of proteins in the soft and hard corona layers of PLGA and PCL NPs. NPs were prepared via a single emulsion-solvent evaporation technique and characterized with respect to size, zeta potential, surface morphology and hydrophobicity. Protein fluorescence quenching experiments were performed against human serum albumin. The thermodynamics of serum protein binding onto the NPs was studied using isothermal titration calorimetry. Semi-quantitative analysis of proteins in the PC layers was conducted using gel electrophoresis and mass spectrometry using human serum. Our results demonstrated the influence of particle hydrophobicity on the thermodynamics of protein binding. Human serum proteins bind to a greater extent and with greater affinity to PCL NPs than PLGA NPs. Several proteins were detected in the hard and soft corona of the NPs, representing their unique proteome fingerprints. Some proteins were unique to the PCL NPs. We anticipate that our findings will assist with rational design of polymeric NPs for effective drug delivery applications.
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Affiliation(s)
- Myolisi Ndumiso
- School of Pharmacy, University of the Western Cape, Cape Town, South Africa
| | - Nela Buchtová
- CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France
| | - Lizex Husselmann
- Department of Biotechnology, University of the Western Cape, Cape Town, South Africa
| | - Gadija Mohamed
- Department of Biotechnology, University of the Western Cape, Cape Town, South Africa
| | - Ashwil Klein
- Department of Biotechnology, University of the Western Cape, Cape Town, South Africa
| | - Marique Aucamp
- School of Pharmacy, University of the Western Cape, Cape Town, South Africa
| | - David Canevet
- Université d'Angers, Laboratoire MOLTECH-Anjou, UMR CNRS 6200, Angers, France
| | - Sarah D'Souza
- School of Pharmacy, University of the Western Cape, Cape Town, South Africa
| | | | - Frank Boury
- CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France
| | - Admire Dube
- School of Pharmacy, University of the Western Cape, Cape Town, South Africa.
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24
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Xue S, Wang C, Kim YHB, Bian G, Han M, Xu X, Zhou G. Application of high-pressure treatment improves the in vitro protein digestibility of gel-based meat product. Food Chem 2020; 306:125602. [DOI: 10.1016/j.foodchem.2019.125602] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 09/25/2019] [Accepted: 09/25/2019] [Indexed: 11/29/2022]
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25
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Le Large TY, Meijer LL, Paleckyte R, Boyd LN, Kok B, Wurdinger T, Schelfhorst T, Piersma SR, Pham TV, van Grieken NC, Zonderhuis BM, Daams F, van Laarhoven HW, Bijlsma MF, Jimenez CR, Giovannetti E, Kazemier G. Combined Expression of Plasma Thrombospondin-2 and CA19-9 for Diagnosis of Pancreatic Cancer and Distal Cholangiocarcinoma: A Proteome Approach. Oncologist 2020; 25:e634-e643. [PMID: 31943574 PMCID: PMC7160420 DOI: 10.1634/theoncologist.2019-0680] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/22/2019] [Indexed: 12/16/2022] Open
Abstract
Background Minimally invasive diagnostic biomarkers for patients with pancreatic ductal adenocarcinoma (PDAC) and distal cholangiocarcinoma (dCCA) are warranted to facilitate accurate diagnosis. This study identified diagnostic plasma proteins based on proteomics of tumor secretome. Materials and Methods Secretome of tumor and normal tissue was collected after resection of PDAC and dCCA. Differentially expressed proteins were measured by mass spectrometry. Selected candidate biomarkers and carbohydrate antigen 19‐9 (CA19‐9) were validated by enzyme‐linked immunosorbent assay in plasma from patients with PDAC (n = 82), dCCA (n = 29), benign disease (BD; n = 30), and healthy donors (HDs; n = 50). Areas under the curve (AUCs) of receiver operator characteristic curves were calculated to determine the discriminative power. Results In tumor secretome, 696 discriminatory proteins were identified, including 21 candidate biomarkers. Thrombospondin‐2 (THBS2) emerged as promising biomarker. Abundance of THBS2 in plasma from patients with cancer was significantly higher compared to HDs (p < .001, AUC = 0.844). Combined expression of THBS2 and CA19‐9 yielded the optimal discriminatory capacity (AUC = 0.952), similarly for early‐ and late‐stage disease (AUC = 0.971 and AUC = 0.911). Remarkably, this combination demonstrated a power similar to CA19‐9 to discriminate cancer from BD (AUC = 0.764), and THBS2 provided an additive value in patients with high expression levels of bilirubin. Conclusion Our proteome approach identified a promising set of candidate biomarkers. The combined plasma expression of THBS2/CA19‐9 is able to accurately distinguish patients with PDAC or dCCA from HD and BD. Implications for Practice The combined plasma expression of thrombospondin‐2 and carbohydrate antigen 19‐9 is able to accurately diagnose patients with pancreatic cancer and distal cholangiocarcinoma. This will facilitate minimally invasive diagnosis for these patients by distinguishing them from healthy individuals and benign diseases. This article identifies diagnostic plasma proteins to distinguish patients with pancreatic ductal adenocarcinoma and distal cholangiocarcinoma from benign disease and health donors and evaluates these new markers for additive value with CA19‐9 at different disease stages.
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Affiliation(s)
- Tessa Y.S. Le Large
- Department of Surgery, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Center, University of AmsterdamAmsterdamThe Netherlands
| | - Laura L. Meijer
- Department of Surgery, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
| | - Rosita Paleckyte
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
| | - Lenka N.C. Boyd
- Department of Surgery, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
| | - Bart Kok
- Department of Surgery, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
| | - Thomas Wurdinger
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
| | - Tim Schelfhorst
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
| | - Sander R. Piersma
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
| | - Thang V. Pham
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
| | - Nicole C.T. van Grieken
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
| | - Barbara M. Zonderhuis
- Department of Surgery, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
| | - Freek Daams
- Department of Surgery, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
| | - Hanneke W.M. van Laarhoven
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Center, University of AmsterdamAmsterdamThe Netherlands
| | - Maarten F. Bijlsma
- Laboratory of Experimental Oncology and Radiobiology, Cancer Center Amsterdam, Amsterdam University Medical Center, University of AmsterdamAmsterdamThe Netherlands
| | - Connie R. Jimenez
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
| | - Elisa Giovannetti
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
- Cancer Pharmacology Lab, Associazione Italiana per la Ricerca sul Cancro (AIRC) Start‐Up Unit, Fondazione Pisana per la Scienza, University of PisaPisaItaly
| | - Geert Kazemier
- Department of Surgery, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
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26
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Le Large TYS, El Hassouni B, Funel N, Kok B, Piersma SR, Pham TV, Olive KP, Kazemier G, van Laarhoven HWM, Jimenez CR, Bijlsma MF, Giovannetti E. Proteomic analysis of gemcitabine-resistant pancreatic cancer cells reveals that microtubule-associated protein 2 upregulation associates with taxane treatment. Ther Adv Med Oncol 2019; 11:1758835919841233. [PMID: 31205498 PMCID: PMC6535709 DOI: 10.1177/1758835919841233] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 01/23/2019] [Indexed: 12/18/2022] Open
Abstract
Background: Chemoresistance hampers the treatment of patients suffering from pancreatic ductal adenocarcinoma (PDAC). Here we aimed to evaluate the (phospho)proteome of gemcitabine-sensitive and gemcitabine-resistant PDAC cells to identify novel therapeutic targets and predictive biomarkers. Methods: The oncogenic capabilities of gemcitabine-sensitive and resistant PDAC cells were evaluated in vitro and in vivo. Cultured cells were analyzed by label-free proteomics. Differential proteins and phosphopeptides were evaluated by gene ontology and for their predictive or prognostic biomarker potential with immunohistochemistry of tissue microarrays. Results: Gemcitabine-resistant cells had increased potential to induce xenograft tumours (p value < 0.001). Differential analyses showed that proteins associated with gemcitabine resistance are correlated with microtubule regulation. Indeed, gemcitabine-resistant cells displayed an increased sensitivity for paclitaxel in vitro (p < 0.001) and nab-paclitaxel had a strong anti-tumour efficacy in vivo. Microtubule-associated protein 2 (MAP2) was found to be highly upregulated (p = 0.002, fold change = 10) and phosphorylated in these resistant cells. Expression of MAP2 was correlated with a poorer overall survival in patients treated with gemcitabine in the palliative (p = 0.037) and adjuvant setting (p = 0.014). Conclusions: These data show an explanation as to why the combination of gemcitabine with nab-paclitaxel is effective in PDAC patients. The identified gemcitabine-resistance marker, MAP2, emerged as a novel prognostic marker in PDAC patients treated with gemcitabine and warrants further clinical investigation.
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Affiliation(s)
- Tessa Ya Sung Le Large
- Surgery, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, NetherlandsLEXOR, Center for Experimental and Molecular Medicine, Amsterdam UMC, University of Amsterdam, Cancer Center Amsterdam, Amsterdam, NetherlandsCancer Pharmacology Lab, AIRC-Start-Up, University Hospital of Pisa, Pisa, Italy
| | - Btissame El Hassouni
- Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Niccola Funel
- Cancer Pharmacology Lab, AIRC-Start-Up, University Hospital of Pisa, Pisa, Italy
| | - Bart Kok
- Surgery, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Sander R Piersma
- Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Thang V Pham
- Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Kenneth P Olive
- Departments of Medicine and Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York City, NY, USA
| | - Geert Kazemier
- Surgery, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Hanneke W M van Laarhoven
- Medical Oncology, Amsterdam UMC, University of Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Connie R Jimenez
- Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Maarten F Bijlsma
- LEXOR, Center for Experimental and Molecular Medicine, Amsterdam UMC, University of Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Elisa Giovannetti
- Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands
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27
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Böttger F, Schaaij-Visser TB, de Reus I, Piersma SR, Pham TV, Nagel R, Brakenhoff RH, Thunnissen E, Smit EF, Jimenez CR. Proteome analysis of non-small cell lung cancer cell line secretomes and patient sputum reveals biofluid biomarker candidates for cisplatin response prediction. J Proteomics 2019; 196:106-119. [DOI: 10.1016/j.jprot.2019.01.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/16/2019] [Accepted: 01/29/2019] [Indexed: 12/13/2022]
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28
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Jin Y, Wen M, Yuan Q, Zhang J, Tan W. Beneficial effects of Coomassie staining on proteomic analysis employing PAGE separation followed with whole-gel slicing, in-gel digestion and quantitative LC-MS/MS. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1110-1111:25-35. [DOI: 10.1016/j.jchromb.2019.01.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 01/12/2023]
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29
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Bian WX, Xie Y, Wang XN, Xu GH, Fu BS, Li S, Long G, Zhou X, Zhang XL. Binding of cellular nucleolin with the viral core RNA G-quadruplex structure suppresses HCV replication. Nucleic Acids Res 2019; 47:56-68. [PMID: 30462330 PMCID: PMC6326805 DOI: 10.1093/nar/gky1177] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 10/22/2018] [Accepted: 11/16/2018] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus (HCV) infection is a major cause of human chronic liver disease and hepatocellular carcinoma. G-quadruplex (G4) is an important four-stranded secondary structure of nucleic acids. Recently, we discovered that the core gene of HCV contains a G4 RNA structure; however, the interaction between the HCV core RNA G4 and host cellular proteins, and the roles of the HCV core RNA G4 in HCV infection and pathogenesis remain elusive. Here, we identified a cellular protein, nucleolin (NCL), which bound and stabilized the HCV core RNA G4 structure. We demonstrated the direct interaction and colocalization between NCL and wild-type core RNA G4 at both in vitro and in cell physiological conditions of the alive virus; however no significant interaction was found between NCL and G4-modified core RNA. NCL is also associated with HCV particles. HCV infection induced NCL mRNA and protein expression, while NCL suppressed wild-type viral replication and expression, but not G4-modified virus. Silencing of NCL greatly enhanced viral RNA replication. Our findings provide new insights that NCL may act as a host factor for anti-viral innate immunity, and binding of cellular NCL with the viral core RNA G4 structure is involved in suppressing HCV replication.
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Affiliation(s)
- Wen-Xiu Bian
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Medical Research Institute and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan 430071, PR China
| | - Yan Xie
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Medical Research Institute and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan 430071, PR China
| | - Xiao-Ning Wang
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guo-Hua Xu
- Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
| | - Bo-Shi Fu
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei Province, Wuhan 430072, China
| | - Shu Li
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Medical Research Institute and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan 430071, PR China
| | - Gang Long
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei Province, Wuhan 430072, China
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Medical Research Institute and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan 430071, PR China
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30
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Murphy S, Henry M, Meleady P, Ohlendieck K. Utilization of dried and long-term stored polyacrylamide gels for the advanced proteomic profiling of mitochondrial contact sites from rat liver. Biol Methods Protoc 2018; 3:bpy008. [PMID: 32161802 PMCID: PMC6994098 DOI: 10.1093/biomethods/bpy008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/07/2018] [Accepted: 07/24/2018] [Indexed: 11/25/2022] Open
Abstract
Following subcellular fractionation, the complexity of proteins derived from a particular cellular compartment is often evaluated by gel electrophoretic analysis. For the proteomic cataloguing of these distinct protein populations and their biochemical characterization, gel electrophoretic protein separation can be conveniently combined with liquid chromatography mass spectrometry. Here we describe a gel-enhanced liquid chromatography mass spectrometry (GeLC-MS)/MS approach with a new bioanalytical focus on the proteomic profiling of mitochondrial contact sites from rat liver using the highly sensitive Orbitrap Fusion Tribrid mass spectrometer for optimum protein identification following extraction from dried and long-term stored gels. Mass spectrometric analysis identified 964 protein species in the mitochondrial contact site fraction, whereby 459 proteins were identified by ≥3 unique peptides. This included mitochondrial components of the supramolecular complexes that form the ATP synthase, the respiratory chain, ribosomal subunits and the cytochrome P450 system, as well as crucial components of the translocase complexes translocase of the inner membrane (TIM) and translocase of the outer membrane (TOM) of the two mitochondrial membranes. Proteomics also identified contact site markers, such as glutathione transferase, monoamine oxidase and the pore protein voltage dependent anion channel (VDAC)-1. Hence, this report demonstrates that the GeLC-MS/MS method can be used to study complex mixtures of proteins that have been embedded and stored in dried polyacrylamide gels for a long period of time. Careful re-swelling and standard in-gel digestion is suitable to produce peptide profiles from old gels that can be used to extract sophisticated proteomic maps and enable the subsequent bioinformatics analysis of the distribution of protein function and the determination of potential protein clustering within the contact site system.
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Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
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31
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Changes in the urinary extracellular vesicle proteome are associated with nephronophthisis-related ciliopathies. J Proteomics 2018; 192:27-36. [PMID: 30071318 DOI: 10.1016/j.jprot.2018.07.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 05/17/2018] [Accepted: 07/16/2018] [Indexed: 12/11/2022]
Abstract
Nephronophthisis is one of the leading genetic causes of end-stage renal disease in childhood. Early diagnostics and prognostics for nephronophthisis are currently limited. We aimed to identify non-invasive protein biomarkers for nephronophthisis in urinary extracellular vesicles. Extracellular vesicles were isolated from urine of 12 patients with a nephronophthisis-related ciliopathy and 12 age- and gender-matched controls, followed by in-depth label-free LC-MS/MS proteomics analysis of gel fractionated extracellular vesicle proteins. Supervised cluster analysis of proteomic profiles separated patients from controls. We identified 156 differentially expressed proteins with fold change ≥4 in patients compared to controls (P < .05). Importantly, expression levels of discriminating proteins were correlated with chronic kidney disease stage, suggesting possible applications for urinary extracellular vesicle biomarkers in prognostics for nephronophthisis. Enrichment analysis of gene ontology terms revealed GO terms including signaling, actin cytoskeleton and endocytosis among the downregulated proteins in patients, whereas terms related to response to wounding and extracellular matrix organization were enriched among upregulated proteins. Our findings represent the first step towards a non-invasive diagnostic test for nephronophthisis. Further research is needed to determine specificity of the candidate biomarkers. In conclusion, proteomic profiles of urinary extracellular vesicles differentiate nephronophthisis-related ciliopathy patients from healthy controls. SIGNIFICANCE: Nephronophthisis is an important cause of end-stage renal disease in children and is associated with an average diagnostic delay of 3.5 years. This is the first study investigating candidate biomarkers for nephronophthisis using global proteomics analysis of urinary extracellular vesicles in patients with nephronophthisis compared to control individuals. We show that measuring protein markers in urinary extracellular vesicles is a promising approach for non-invasive early diagnostics of nephronophthisis.
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32
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Wang G, Ma F, Zeng L, Bai Y, Wang H, Xu X, Zhou G. Modified atmosphere packaging decreased Pseudomonas fragi cell metabolism and extracellular proteolytic activities on meat. Food Microbiol 2018; 76:443-449. [PMID: 30166172 DOI: 10.1016/j.fm.2018.07.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 07/09/2018] [Accepted: 07/16/2018] [Indexed: 10/28/2022]
Abstract
Modified atmosphere packaging (MAP) is considered an effective method for extending the shelf life of meat. The use of optimal mixture of gases (CO2 and N2) in food packaging containers has been proved to effectively inhibit the growth of microorganisms in poultry meat. In general, a minimum CO2 concentration range of 20%-30% is required for the inhibitory effect. The aim of this study was to investigate the mechanism by which MAP (CO2/N2 30%/70%) inhibits Pseudomonas fragi, a dominant spoilage microorganism in aerobically stored chilled meat. The cell physiological changes were determined by measuring membrane integrity, membrane potential, ATP level, and extracellular proteolytic activity. The results showed that samples stored under MA retained cell membrane integrity, but lost significant membrane potential and ATP synthesis activity. Furthermore, the peptides issued from 2 structural proteins (myosin and actin) were mainly identified in air samples, indicating that these fragments result from bacterial proteolytic activity while MAP inhibited this activity. Overall, the study found that cell metabolism and extracellular protease activity decreased under MAP conditions. This study showed that MAP is an effective food preservation strategy and revealed mechanisms by which MAP inhibits spoilage.
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Affiliation(s)
- Guangyu Wang
- Key Laboratory of Meat Processing and Quality Control, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Fang Ma
- College of Veterinary Medicine, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, PR China
| | - Leyin Zeng
- Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, PR China
| | - Yun Bai
- Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, PR China
| | - Huhu Wang
- Key Laboratory of Meat Processing and Quality Control, Nanjing Agricultural University, Nanjing, Jiangsu, PR China.
| | - Xinglian Xu
- Key Laboratory of Meat Processing and Quality Control, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Guanghong Zhou
- Key Laboratory of Meat Processing and Quality Control, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
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33
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Sabrkhany S, Kuijpers MJE, Knol JC, Olde Damink SWM, Dingemans AMC, Verheul HM, Piersma SR, Pham TV, Griffioen AW, Oude Egbrink MGA, Jimenez CR. Exploration of the platelet proteome in patients with early-stage cancer. J Proteomics 2018; 177:65-74. [PMID: 29432918 DOI: 10.1016/j.jprot.2018.02.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 12/29/2017] [Accepted: 02/05/2018] [Indexed: 02/07/2023]
Abstract
Platelets play an important role in tumor growth and, at the same time, platelet characteristics are affected by cancer presence. Therefore, we investigated whether the platelet proteome harbors differentially expressed proteins associated with early-stage cancer. For this proof-of-concept study, patients with early-stage lung (n = 8) or head of pancreas cancer (n = 4) were included, as were healthy sex- and age-matched controls for both subgroups. Blood samples were collected from controls and from patients before surgery. Furthermore, from six of the patients, a second sample was collected two months after surgery. NanoLC-MS/MS-based proteomics of gel-fractionated platelet proteins was used for comparative spectral count analyses of patients to controls and before to after surgery samples. The total platelet proteome dataset included 4384 unique proteins of which 85 were significantly (criteria Fc > 1.5 and p < 0.05) changed in early-stage cancer compared to controls. In addition, the levels of 81 platelet proteins normalized after tumor resection. When filtering for the most discriminatory proteins, we identified seven promising platelet proteins associated with early-stage cancer. In conclusion, this pioneering study on the platelet proteome in cancer patients clearly identifies platelets as a new source of candidate protein biomarkers of early-stage cancer. BIOLOGICAL SIGNIFICANCE Currently, most blood-based diagnostics/biomarker research is performed in serum or plasma, while the content of blood cells is usually neglected. It is known that especially blood platelets, which are the main circulating pool of many bioactive proteins, such as growth factors, chemokines, and cytokines, are a potentially rich source of biomarkers. The current study is the first to measure the effect of early-stage cancer on the platelet proteome of patients. Our study demonstrates that the platelet proteome of patients with early-stage lung or head of pancreas cancer differs considerably compared to that of healthy individuals of matched sex and age. In addition, the platelet proteome of cancer patients normalized after surgical resection of the tumor. Exploiting platelet proteome differences linked to both tumor presence and disease status, we were able to demonstrate that the platelet proteome can be mined for potential biomarkers of cancer.
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Affiliation(s)
- Siamack Sabrkhany
- Cardiovascular Research Institute Maastricht, Department of Physiology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Marijke J E Kuijpers
- Cardiovascular Research Institute Maastricht, Department of Biochemistry, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jaco C Knol
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, VU Medical Center, Amsterdam, The Netherlands
| | - Steven W M Olde Damink
- Cardiovascular Research Institute Maastricht, Department of Surgery, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Anne-Marie C Dingemans
- Cardiovascular Research Institute Maastricht, Department of Pulmonology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Henk M Verheul
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, VU Medical Center, Amsterdam, The Netherlands
| | - Sander R Piersma
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, VU Medical Center, Amsterdam, The Netherlands
| | - Thang V Pham
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, VU Medical Center, Amsterdam, The Netherlands
| | - Arjan W Griffioen
- Angiogenesis Laboratory, Department of Medical Oncology, VU Medical Center, Amsterdam, The Netherlands
| | - Mirjam G A Oude Egbrink
- Cardiovascular Research Institute Maastricht, Department of Physiology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Connie R Jimenez
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, VU Medical Center, Amsterdam, The Netherlands.
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34
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Feist PE, Loughran EA, Stack MS, Hummon AB. Quantitative proteomic analysis of murine white adipose tissue for peritoneal cancer metastasis. Anal Bioanal Chem 2017; 410:1583-1594. [PMID: 29282499 DOI: 10.1007/s00216-017-0813-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/30/2017] [Accepted: 12/06/2017] [Indexed: 12/15/2022]
Abstract
Cancer metastasis risk increases in older individuals, but the mechanisms for this risk increase are unclear. Many peritoneal cancers, including ovarian cancer, preferentially metastasize to peritoneal fat depots. However, there is a dearth of studies exploring aged peritoneal adipose tissue in the context of cancer. Because adipose tissue produces signals which influence several diseases including cancer, proteomics of adipose tissue in aged and young mice may provide insight into metastatic mechanisms. We analyzed mesenteric, omental, and uterine adipose tissue groups from the peritoneal cavities of young and aged C57BL/6J mouse cohorts with a low-fraction SDS-PAGE gelLC-MS/MS method. We identified 2308 protein groups and quantified 2167 groups, among which several protein groups showed twofold or greater abundance differences between the aged and young cohorts. Cancer-related gene products previously identified as significant in another age-related study were found altered in this study. Several gene products known to suppress proliferation and cellular invasion were found downregulated in the aged cohort, including R-Ras, Arid1a, and heat shock protein β1. In addition, multiple protein groups were identified within single cohorts, including the proteins Cd11a, Stat3, and Ptk2b. These data suggest that adipose tissue is a strong candidate for analysis to identify possible contributors to cancer metastasis in older subjects. The results of this study, the first of its kind using uterine adipose tissue, contribute to the understanding of the role of adipose tissue in age-related alteration of oncogenic pathways, which may help elucidate the mechanisms of increased metastatic tumor burden in the aged. Graphical abstract We analyzed mesenteric, omental, and uterine adipose tissue groups from the peritoneal cavities of young and aged C57BL/6J mouse cohorts with a low-fraction SDS-PAGE gelLC-MS/MS method. These fat depots are preferential sites for many peritoneal cancers. The results of this study, the first of its kind using uterine adipose tissue, contribute to the understanding of the role of adipose tissue in age-related alteration of oncogenic pathways, which may help elucidate the mechanisms of increased metastatic tumor burden in the aged.
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Affiliation(s)
- Peter E Feist
- Integrated Biomedical Sciences Program, University of Notre Dame, Notre Dame, IN, 46556, USA
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, 251 140B McCourtney Hall, Notre Dame, IN, 46556, USA
| | - Elizabeth A Loughran
- Integrated Biomedical Sciences Program, University of Notre Dame, Notre Dame, IN, 46556, USA
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, 251 140B McCourtney Hall, Notre Dame, IN, 46556, USA
| | - M Sharon Stack
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, 251 140B McCourtney Hall, Notre Dame, IN, 46556, USA
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, 251 140B McCourtney Hall, Notre Dame, IN, 46556, USA.
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35
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Kumar M, Joseph SR, Augsburg M, Bogdanova A, Drechsel D, Vastenhouw NL, Buchholz F, Gentzel M, Shevchenko A. MS Western, a Method of Multiplexed Absolute Protein Quantification is a Practical Alternative to Western Blotting. Mol Cell Proteomics 2017; 17:384-396. [PMID: 29192002 DOI: 10.1074/mcp.o117.067082] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 10/12/2017] [Indexed: 12/23/2022] Open
Abstract
Absolute quantification of proteins elucidates the molecular composition, regulation and dynamics of multiprotein assemblies and networks. Here we report on a method termed MS Western that accurately determines the molar abundance of dozens of user-selected proteins at the subfemtomole level in whole cell or tissue lysates without metabolic or chemical labeling and without using specific antibodies. MS Western relies on GeLC-MS/MS and quantifies proteins by in-gel codigestion with an isotopically labeled QconCAT protein chimera composed of concatenated proteotypic peptides. It requires no purification of the chimera and relates the molar abundance of all proteotypic peptides to a single reference protein. In comparative experiments, MS Western outperformed immunofluorescence Western blotting by the protein detection specificity, linear dynamic range and sensitivity of protein quantification. To validate MS Western in an in vivo experiment, we quantified the molar content of zebrafish core histones H2A, H2B, H3 and H4 during ten stages of early embryogenesis. Accurate quantification (CV<10%) corroborated the anticipated histones equimolar stoichiometry and revealed an unexpected trend in their total abundance.
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Affiliation(s)
- Mukesh Kumar
- From the ‡Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Shai R Joseph
- From the ‡Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Martina Augsburg
- §Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Aliona Bogdanova
- From the ‡Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - David Drechsel
- From the ‡Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Nadine L Vastenhouw
- From the ‡Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Frank Buchholz
- From the ‡Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.,§Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany.,¶German Cancer Research Center (DKFZ), Heidelberg and German Cancer Consortium (DKTK) partner site Dresden, 01307 Dresden, Germany.,‖National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Marc Gentzel
- From the ‡Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Andrej Shevchenko
- From the ‡Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany;
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36
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Comparative proteome and peptidome analysis of the cephalic fluid secreted by Arapaima gigas (Teleostei: Osteoglossidae) during and outside parental care. PLoS One 2017; 12:e0186692. [PMID: 29065179 PMCID: PMC5655490 DOI: 10.1371/journal.pone.0186692] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 10/05/2017] [Indexed: 02/05/2023] Open
Abstract
Parental investment in Arapaima gigas includes nest building and guarding, followed by a care provision when a cephalic fluid is released from the parents’ head to the offspring. This fluid has presumably important functions for the offspring but so far its composition has not been characterised. In this study the proteome and peptidome of the cephalic secretion was studied in parental and non-parental fish using capillary electrophoresis coupled to mass spectrometry (CE-MS) and GeLC-MS/MS analyses. Multiple comparisons revealed 28 peptides were significantly different between males and parental males (PC-males), 126 between females and parental females (PC-females), 51 between males and females and 9 between PC-males and PC-females. Identification revealed peptides were produced in the inner ear (pcdh15b), eyes (tetraspanin and ppp2r3a), central nervous system (otud4, ribeye a, tjp1b and syn1) among others. A total of 422 proteins were also identified and gene ontology analysis revealed 28 secreted extracellular proteins. From these, 2 hormones (prolactin and stanniocalcin) and 12 proteins associated to immunological processes (serotransferrin, α-1-antitrypsin homolog, apolipoprotein A-I, and others) were identified. This study provides novel biochemical data on the lateral line fluid which will enable future hypotheses-driven experiments to better understand the physiological roles of the lateral line in chemical communication.
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37
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Wen M, Jin Y, Manabe T, Chen S, Tan W. A comparative analysis of human plasma and serum proteins by combining native PAGE, whole-gel slicing and quantitative LC-MS/MS: Utilizing native MS-electropherograms in proteomic analysis for discovering structure and interaction-correlated differences. Electrophoresis 2017; 38:3111-3123. [DOI: 10.1002/elps.201700261] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/09/2017] [Accepted: 08/28/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Meiling Wen
- School of Bioscience and Bioengineering; South China University of Technology; Guangzhou P. R. China
| | - Ya Jin
- Institute of Biomedical and Pharmaceutical Sciences; Guangdong University of Technology; Guangzhou P. R. China
| | | | - Shumin Chen
- School of Bioscience and Bioengineering; South China University of Technology; Guangzhou P. R. China
| | - Wen Tan
- Institute of Biomedical and Pharmaceutical Sciences; Guangdong University of Technology; Guangzhou P. R. China
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38
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Kardoush MI, Ward BJ, Ndao M. Serum Carbonic Anhydrase 1 is a Biomarker for Diagnosis of Human Schistosoma mansoni Infection. Am J Trop Med Hyg 2017; 96:842-849. [PMID: 28500821 DOI: 10.4269/ajtmh.16-0021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
AbstractSchistosoma mansoni is a major public health threat in many parts of the world. The current diagnostic tests for schistosomiasis are suboptimal, particularly early in infection, when the parasite burden is low and with reinfection after treatment. We sought to identify novel biomarkers of active infection by studying serum proteins in a mouse model of schistosomiasis followed by confirmation in chronically infected patients. Acute (6 weeks) and chronic (12 weeks) sera from S. mansoni-infected C57Bl/6 mice as well as sera from chronically infected patients were assessed using two proteomic platforms: surface-enhanced, laser desorption and ionization, time-of-flight mass spectrometry and Velos Orbitrap mass spectrometry. Several candidate biomarkers were further evaluated by Western blot and/or enzyme-linked immunosorbent assay (ELISA). Among the most promising was carbonic anhydrase 1 (CA1), a host protein found primarily in red blood cells and enterocytes that proved to be a negative biomarker for schistosomiasis in both mouse and human samples. Reduced serum CA-1 levels were confirmed by both Western blot (murine and human: both P < 0.001) and ELISA (human: P < 0.01). Western blots of serial mouse sera revealed a progressive reduction in serum CA1 levels over the 12-week infection period. CA1 is a promising negative serum biomarker for the diagnosis of S. mansoni infection.
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Affiliation(s)
- Manal Ibrahim Kardoush
- Department of Parasitology, Faculty of Medicine, Benha University, Benha, Egypt.,National Reference Center for Parasitology, Research Institute of the McGill University Health Center, Montreal, Canada.,Institute of Parasitology, McGill University, Montreal, Canada
| | - Brian J Ward
- Department of Experimental Medicine, McGill University, Montreal, Canada.,National Reference Center for Parasitology, Research Institute of the McGill University Health Center, Montreal, Canada
| | - Momar Ndao
- National Reference Center for Parasitology, Research Institute of the McGill University Health Center, Montreal, Canada.,Department of Experimental Medicine, McGill University, Montreal, Canada
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39
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Komor MA, Pham TV, Hiemstra AC, Piersma SR, Bolijn AS, Schelfhorst T, Delis-van Diemen PM, Tijssen M, Sebra RP, Ashby M, Meijer GA, Jimenez CR, Fijneman RJA. Identification of Differentially Expressed Splice Variants by the Proteogenomic Pipeline Splicify. Mol Cell Proteomics 2017; 16:1850-1863. [PMID: 28747380 DOI: 10.1074/mcp.tir117.000056] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Indexed: 12/20/2022] Open
Abstract
Proteogenomics, i.e. comprehensive integration of genomics and proteomics data, is a powerful approach identifying novel protein biomarkers. This is especially the case for proteins that differ structurally between disease and control conditions. As tumor development is associated with aberrant splicing, we focus on this rich source of cancer specific biomarkers. To this end, we developed a proteogenomic pipeline, Splicify, which can detect differentially expressed protein isoforms. Splicify is based on integrating RNA massive parallel sequencing data and tandem mass spectrometry proteomics data to identify protein isoforms resulting from differential splicing between two conditions. Proof of concept was obtained by applying Splicify to RNA sequencing and mass spectrometry data obtained from colorectal cancer cell line SW480, before and after siRNA-mediated downmodulation of the splicing factors SF3B1 and SRSF1. These analyses revealed 2172 and 149 differentially expressed isoforms, respectively, with peptide confirmation upon knock-down of SF3B1 and SRSF1 compared with their controls. Splice variants identified included RAC1, OSBPL3, MKI67, and SYK. One additional sample was analyzed by PacBio Iso-Seq full-length transcript sequencing after SF3B1 downmodulation. This analysis verified the alternative splicing identified by Splicify and in addition identified novel splicing events that were not represented in the human reference genome annotation. Therefore, Splicify offers a validated proteogenomic data analysis pipeline for identification of disease specific protein biomarkers resulting from mRNA alternative splicing. Splicify is publicly available on GitHub (https://github.com/NKI-TGO/SPLICIFY) and suitable to address basic research questions using pre-clinical model systems as well as translational research questions using patient-derived samples, e.g. allowing to identify clinically relevant biomarkers.
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Affiliation(s)
- Malgorzata A Komor
- From the ‡Translational Gastrointestinal Oncology, Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands.,§Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - Thang V Pham
- §Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - Annemieke C Hiemstra
- From the ‡Translational Gastrointestinal Oncology, Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Sander R Piersma
- §Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - Anne S Bolijn
- From the ‡Translational Gastrointestinal Oncology, Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Tim Schelfhorst
- §Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - Pien M Delis-van Diemen
- From the ‡Translational Gastrointestinal Oncology, Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Marianne Tijssen
- From the ‡Translational Gastrointestinal Oncology, Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Robert P Sebra
- ¶School of Medicine at Mount Sinai, Institute for Genomics and Multiscale Biology, New York, New York
| | | | - Gerrit A Meijer
- From the ‡Translational Gastrointestinal Oncology, Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Connie R Jimenez
- §Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - Remond J A Fijneman
- From the ‡Translational Gastrointestinal Oncology, Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands;
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40
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Bridel C, Koel-Simmelink MJA, Peferoen L, Derada Troletti C, Durieux S, Gorter R, Nutma E, Gami P, Iacobaeus E, Brundin L, Kuhle J, Vrenken H, Killestein J, Piersma SR, Pham TV, De Vries HE, Amor S, Jimenez CR, Teunissen CE. Brain endothelial cell expression of SPARCL-1 is specific to chronic multiple sclerosis lesions and is regulated by inflammatory mediators in vitro. Neuropathol Appl Neurobiol 2017; 44:404-416. [PMID: 28543098 DOI: 10.1111/nan.12412] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 05/18/2017] [Accepted: 05/24/2017] [Indexed: 02/05/2023]
Abstract
AIMS Cell matrix modulating protein SPARCL-1 is highly expressed by astrocytes during CNS development and following acute CNS damage. Applying NanoLC-MS/MS to CSF of RRMS and SPMS patients, we identified SPARCL-1 as differentially expressed between these two stages of MS, suggesting a potential as CSF biomarker to differentiate RRMS from SPMS and a role in MS pathogenesis. METHODS This study examines the potential of SPARCL-1 as CSF biomarker discriminating RRMS from SPMS in three independent cohorts (n = 249), analyses its expression pattern in MS lesions (n = 26), and studies its regulation in cultured human brain microvasculature endothelial cells (BEC) after exposure to MS-relevant inflammatory mediators. RESULTS SPARCL-1 expression in CSF was significantly higher in SPMS compared to RRMS in a Dutch cohort of 76 patients. This finding was not replicated in 2 additional cohorts of MS patients from Sweden (n = 81) and Switzerland (n = 92). In chronic MS lesions, but not active lesions or NAWM, a vessel expression pattern of SPARCL-1 was observed in addition to the expression by astrocytes. EC were found to express SPARCL-1 in chronic MS lesions, and SPARCL-1 expression was regulated by MS-relevant inflammatory mediators in cultured human BEC. CONCLUSIONS Conflicting results of SPARCL-1's differential expression in CSF of three independent cohorts of RRMS and SPMS patients precludes its use as biomarker for disease progression. The expression of SPARCL-1 by BEC in chronic MS lesions together with its regulation by inflammatory mediators in vitro suggest a role for SPARCL-1 in MS neuropathology, possibly at the brain vascular level.
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Affiliation(s)
- C Bridel
- Department of Clinical Chemistry, Neurochemistry Lab and Biobank, VU Medical Centre, Amsterdam, The Netherlands
| | - M J A Koel-Simmelink
- Department of Clinical Chemistry, Neurochemistry Lab and Biobank, VU Medical Centre, Amsterdam, The Netherlands
| | - L Peferoen
- Department of Pathology, VU Medical Centre, Amsterdam, The Netherlands
| | - C Derada Troletti
- Department of Molecular Cell Biology and Immunology, Neuroscience Campus Amsterdam, VU University Medical Centre, Amsterdam, The Netherlands
| | - S Durieux
- Department of Clinical Chemistry, Neurochemistry Lab and Biobank, VU Medical Centre, Amsterdam, The Netherlands
| | - R Gorter
- Department of Pathology, VU Medical Centre, Amsterdam, The Netherlands
| | - E Nutma
- Department of Pathology, VU Medical Centre, Amsterdam, The Netherlands
| | - P Gami
- Department of Pathology, VU Medical Centre, Amsterdam, The Netherlands
| | - E Iacobaeus
- Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institute, Solna, Sweden.,Center for Molecular Medicine, Stockholm, Sweden
| | - L Brundin
- Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institute, Solna, Sweden.,Center for Molecular Medicine, Stockholm, Sweden
| | - J Kuhle
- Neurology, Department of Medicine, Biomedicine and Clinical Research, University Hospital Basel, Basel, Switzerland
| | - H Vrenken
- Department of Radiology and Nuclear Medicine and Department of Physics and Medical Technology, VU University Medical Center, Amsterdam, The Netherlands
| | - J Killestein
- Department of Neurology, MS Centre Amsterdam, VU Medical Centre, Amsterdam, The Netherlands
| | - S R Piersma
- Department of Medical Oncology, OncoProteomics Laboratory, VU Medical Centre, Amsterdam, The Netherlands
| | - T V Pham
- Department of Medical Oncology, OncoProteomics Laboratory, VU Medical Centre, Amsterdam, The Netherlands
| | - H E De Vries
- Department of Molecular Cell Biology and Immunology, Neuroscience Campus Amsterdam, VU University Medical Centre, Amsterdam, The Netherlands
| | - S Amor
- Department of Pathology, VU Medical Centre, Amsterdam, The Netherlands.,Queen Mary University of London, Blizard Institute, Barts and The London School of Medicine and Dentistry, London, UK
| | - C R Jimenez
- Department of Medical Oncology, OncoProteomics Laboratory, VU Medical Centre, Amsterdam, The Netherlands
| | - C E Teunissen
- Department of Clinical Chemistry, Neurochemistry Lab and Biobank, VU Medical Centre, Amsterdam, The Netherlands
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41
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Baloyi NM, Dubery IA, Piater LA. Proteomic analysis of Arabidopsis plasma membranes reveals lipopolysaccharide-responsive changes. Biochem Biophys Res Commun 2017; 486:1137-1142. [PMID: 28390899 DOI: 10.1016/j.bbrc.2017.04.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 04/04/2017] [Indexed: 11/24/2022]
Abstract
Plant plasma membranes (PMs) contain pattern recognition receptors (PRRs), lately believed to be associated within multicomponent complexes, which perceive microbe-associated molecular pattern (MAMP) molecules like lipopolysaccharides (LPSs) and result in signal transduction events that lead to activated immune defense responses. As such, Arabidopsis thaliana leaves were treated with LPS from Escherichia coli (LPSE.coli) over time, and PM fractions isolated and evaluated using gel-based and subsequent mass spectrometry approaches for identification of LPS-responsive proteins. From the identified protein bands and spots, it is concluded that perception of hexaacylated LPS and resulting signal transduction occurs via PM-associated protein(s), amongst others, receptor-like kinases (RLKs) including G-type lectin S-receptor kinase and BAK1, and mostly likely within specialized perception domains.
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Affiliation(s)
- Nwaxigombe M Baloyi
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg, South Africa
| | - Ian A Dubery
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg, South Africa
| | - Lizelle A Piater
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg, South Africa.
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42
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Bijnsdorp IV, Maxouri O, Kardar A, Schelfhorst T, Piersma SR, Pham TV, Vis A, van Moorselaar RJ, Jimenez CR. Feasibility of urinary extracellular vesicle proteome profiling using a robust and simple, clinically applicable isolation method. J Extracell Vesicles 2017; 6:1313091. [PMID: 28717416 PMCID: PMC5505003 DOI: 10.1080/20013078.2017.1313091] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/26/2017] [Indexed: 12/31/2022] Open
Abstract
Extracellular vesicles (EVs) secreted by prostate cancer (PCa) cells contain specific biomarkers and can be isolated from urine. Collection of urine is not invasive, and therefore urinary EVs represent a liquid biopsy for diagnostic and prognostic testing for PCa. In this study, we optimised urinary EV isolation using a method based on heat shock proteins and compared it to gold-standard ultracentrifugation. The urinary EV isolation protocol using the Vn96-peptide is easier, time convenient (≈1.5 h) and no special equipment is needed, in contrast to ultracentrifugation protocol (>3.5 h), making this protocol clinically feasible. We compared the isolated vesicles of both ultracentrifugation and Vn96-peptide by proteome profiling using mass spectrometry-based proteomics (n = 4 per method). We reached a depth of >3000 proteins, with 2400 proteins that were commonly detected in urinary EVs from different donors. We show a large overlap (>85%) between proteins identified in EVs isolated by ultracentrifugation and Vn96-peptide. Addition of the detergent NP40 to Vn96-peptide EV isolations reduced levels of background proteins and highly increased the levels of the EV-markers TSG101 and PDCD6IP, indicative of an increased EV yield. Thus, the Vn96-peptide-based EV isolation procedure is clinically feasibly and allows large-scale protein profiling of urinary EV biomarkers.
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Affiliation(s)
- Irene V Bijnsdorp
- Department of Urology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Olga Maxouri
- Department of Urology, VU University Medical Centre, Amsterdam, The Netherlands.,Department of Medical Oncology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Aarzo Kardar
- Department of Urology, VU University Medical Centre, Amsterdam, The Netherlands.,Department of Medical Oncology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Tim Schelfhorst
- Department of Medical Oncology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Andre Vis
- Department of Urology, VU University Medical Centre, Amsterdam, The Netherlands
| | | | - Connie R Jimenez
- Department of Medical Oncology, VU University Medical Centre, Amsterdam, The Netherlands
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43
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Boyatzis AE, Bringans SD, Piggott MJ, Duong MN, Lipscombe RJ, Arthur PG. Limiting the Hydrolysis and Oxidation of Maleimide–Peptide Adducts Improves Detection of Protein Thiol Oxidation. J Proteome Res 2017; 16:2004-2015. [DOI: 10.1021/acs.jproteome.6b01060] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Amber E. Boyatzis
- School
of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia 6009, Australia
| | | | - Matthew J. Piggott
- School
of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Marisa N. Duong
- School
of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia 6009, Australia
| | | | - Peter G. Arthur
- School
of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia 6009, Australia
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44
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Application of nano-LC-MALDI-TOF/TOF-MS for proteomic analysis of microvesicles. Clin Biochem 2017; 50:241-243. [DOI: 10.1016/j.clinbiochem.2016.11.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 11/12/2016] [Accepted: 11/12/2016] [Indexed: 12/29/2022]
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45
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Xiang T, Yang G, Liu X, Zhou Y, Fu Z, Lu F, Gu J, Taniguchi N, Tan Z, Chen X, Xie Y, Guan F, Zhang XL. Alteration of N-glycan expression profile and glycan pattern of glycoproteins in human hepatoma cells after HCV infection. Biochim Biophys Acta Gen Subj 2017; 1861:1036-1045. [PMID: 28229927 DOI: 10.1016/j.bbagen.2017.02.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 02/09/2017] [Accepted: 02/11/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND Hepatitis C virus (HCV) infection causes chronic liver diseases, liver fibrosis and even hepatocellular carcinoma (HCC). However little is known about any information of N-glycan pattern in human liver cell after HCV infection. METHODS The altered profiles of N-glycans in HCV-infected Huh7.5.1 cell were analyzed by using mass spectrometry. Then, lectin microarray, lectin pull-down assay, reverse transcription-quantitative real time PCR (RT-qPCR) and western-blotting were used to identify the altered N-glycosylated proteins and glycosyltransferases. RESULTS Compared to uninfected cells, significantly elevated levels of fucosylated, sialylated and complex N-glycans were found in HCV infected cells. Furthermore, Lens culinaris agglutinin (LCA)-binding glycoconjugates were increased most. Then, the LCA-agarose was used to precipitate the specific glycosylated proteins and identify that fucosylated modified annexin A2 (ANXA2) and heat shock protein 90 beta family member 1 (HSP90B1) was greatly increased in HCV-infected cells. However, the total ANXA2 and HSP90B1 protein levels remained unchanged. Additionally, we screened the mRNA expressions of 47 types of different glycosyltransferases and found that α1,6-fucosyltransferase 8 (FUT8) was the most up-regulated and contributed to strengthen the LCA binding capability to fucosylated modified ANXA2 and HSP90B1 after HCV infection. CONCLUSIONS HCV infection caused the altered N-glycans profiles, increased expressions of FUT8, fucosylated ANXA2 and HSP90B1 as well as enhanced LCA binding to Huh7.5.1. GENERAL SIGNIFICANCE Our results may lay the foundation for clarifying the role of N-glycans and facilitate the development of novel diagnostic biomarkers and therapeutic targets based on the increased FUT8, fucosylated ANXA2 and HSP90B1 after HCV infection.
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Affiliation(s)
- Tian Xiang
- State Key Laboratory of Virology. Hubei province Key Laboratory of Allergy and Immune-related diseases, Medical Research Institute, Department of Immunology of Wuhan University School of Basic Medical Sciences, Wuhan 430071, China
| | - Ganglong Yang
- The Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xiaoyu Liu
- State Key Laboratory of Virology. Hubei province Key Laboratory of Allergy and Immune-related diseases, Medical Research Institute, Department of Immunology of Wuhan University School of Basic Medical Sciences, Wuhan 430071, China
| | - Yidan Zhou
- University of Illinois at Urbana-Champaign, School of Molecular and Cellular Biology, Department of Microbiology, IL 61801, USA
| | - Zhongxiao Fu
- State Key Laboratory of Virology. Hubei province Key Laboratory of Allergy and Immune-related diseases, Medical Research Institute, Department of Immunology of Wuhan University School of Basic Medical Sciences, Wuhan 430071, China
| | - Fangfang Lu
- State Key Laboratory of Virology. Hubei province Key Laboratory of Allergy and Immune-related diseases, Medical Research Institute, Department of Immunology of Wuhan University School of Basic Medical Sciences, Wuhan 430071, China
| | - Jianguo Gu
- Division of Regulatory Glycobiology, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aobaku, Sendai, Miyagi 981-8558, Japan
| | - Naoyuki Taniguchi
- Systems Glycobiology Group, Global Research Cluster, RIKEN and RIKEN-Max Planck Joint Research Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Zengqi Tan
- The Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xi Chen
- Wuhan Institute of Biotechnology, Medical Research Institute of Wuhan University, Wuhan 430071, China
| | - Yan Xie
- State Key Laboratory of Virology. Hubei province Key Laboratory of Allergy and Immune-related diseases, Medical Research Institute, Department of Immunology of Wuhan University School of Basic Medical Sciences, Wuhan 430071, China
| | - Feng Guan
- The Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology. Hubei province Key Laboratory of Allergy and Immune-related diseases, Medical Research Institute, Department of Immunology of Wuhan University School of Basic Medical Sciences, Wuhan 430071, China.
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46
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Padrão AI, Ferreira R, Amado F, Vitorino R, Duarte JA. Uncovering the exercise-related proteome signature in skeletal muscle. Proteomics 2016; 16:816-30. [PMID: 26632760 DOI: 10.1002/pmic.201500382] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Revised: 10/13/2015] [Accepted: 11/30/2015] [Indexed: 01/01/2023]
Abstract
Exercise training has been recommended as a nonpharmacological strategy for the prevention and attenuation of skeletal muscle atrophy in distinct pathophysiological conditions. Despite the well-established phenotypic alterations, the molecular mechanisms underlying exercise-induced skeletal muscle remodeling are poorly characterized. Proteomics based on mass spectrometry have been successfully applied for the characterization of skeletal muscle proteome, representing a pivotal approach for the wide characterization of the molecular networks that lead to skeletal muscle remodeling. Nevertheless, few studies were performed to characterize the exercise-induced proteome remodeling of skeletal muscle, with only six research papers focused on the cross-talk between exercise and pathophysiological conditions. In order to add new insights on the impact of distinct exercise programs on skeletal muscle proteome, molecular network analysis was performed with bioinformatics tools. This analysis highlighted an exercise-related proteome signature characterized by the up-regulation of the capacity for ATP generation, oxygen delivery, antioxidant capacity and regulation of mitochondrial protein synthesis. Chronic endurance training up-regulates the tricarboxylic acid cycle and oxidative phosphorylation system, whereas the release of calcium ion into cytosol and amino acid metabolism are the biological processes up-regulated by a single bout of exercise. Other issues as exercise intensity, load, mode and regimen as well as muscle type also influence the exercise-induced proteome signature. The comprehensive analysis of the molecular networks modulated by exercise training in health and disease, taking in consideration all these variables, might not only support the therapeutic effect of exercise but also highlight novel targets for the development of enhanced pharmacological strategies.
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Affiliation(s)
- Ana Isabel Padrão
- QOPNA, Department of Chemistry, University of Aveiro, Aveiro, Portugal.,CIAFEL, Faculty of Sports, University of Porto, Porto, Portugal
| | - Rita Ferreira
- QOPNA, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Francisco Amado
- QOPNA, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Rui Vitorino
- Department of Medical Sciences and Institute for Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal.,Department of Physiology and Cardiothoracic Surgery, Faculty of Medicine, University of Porto, Porto, Portugal
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47
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Knol JC, de Reus I, Schelfhorst T, Beekhof R, de Wit M, Piersma SR, Pham TV, Smit EF, Verheul HM, Jiménez CR. Peptide-mediated 'miniprep' isolation of extracellular vesicles is suitable for high-throughput proteomics. EUPA OPEN PROTEOMICS 2016; 11:11-15. [PMID: 29900106 PMCID: PMC5988555 DOI: 10.1016/j.euprot.2016.02.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/12/2016] [Accepted: 02/16/2016] [Indexed: 01/14/2023]
Abstract
Extracellular vesicles (EVs) are cell-secreted membrane vesicles enclosed by a lipid bilayer derived from endosomes or from the plasma membrane. Since EVs are released into body fluids, and their cargo includes tissue-specific and disease-related molecules, they represent a rich source for disease biomarkers. However, standard ultracentrifugation methods for EV isolation are laborious, time-consuming, and require high inputs. Ghosh and co-workers recently described an isolation method utilizing Heat Shock Protein (HSP)-binding peptide Vn96 to aggregate HSP-decorated EVs, which can be performed at small 'miniprep' scale. Based on microscopic, immunoblot, and RNA sequencing analyses this method compared well with ultracentrifugation-mediated EV isolation, but a detailed proteomic comparison was lacking. Therefore, we compared both methods using label-free proteomics of replicate EV isolations from HT-29 cell-conditioned medium. Despite a 30-fold different scale (ultracentrifugation: 60 ml/Vn96-mediated aggregation: 2 ml) both methods yielded comparable numbers of identified proteins (3115/3085), with similar reproducibility of identification (72.5%/75.5%) and spectral count-based quantification (average CV: 31%/27%). EV fractions obtained with either method contained established EV markers and proteins linked to vesicle-related gene ontologies. Thus, Vn96 peptide-mediated aggregation is an advantageous, simple and rapid approach for EV isolation from small biological samples, enabling high-throughput analysis in a biomarker discovery setting.
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Affiliation(s)
- Jaco C. Knol
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Inge de Reus
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Tim Schelfhorst
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Robin Beekhof
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Meike de Wit
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Sander R. Piersma
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Thang V. Pham
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Egbert F. Smit
- Department of Pulmonary Diseases, VU University Medical Center, The Netherlands
| | - Henk M.W. Verheul
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Connie R. Jiménez
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
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48
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Wojtuszkiewicz A, Schuurhuis GJ, Kessler FL, Piersma SR, Knol JC, Pham TV, Jansen G, Musters RJP, van Meerloo J, Assaraf YG, Kaspers GJL, Zweegman S, Cloos J, Jimenez CR. Exosomes Secreted by Apoptosis-Resistant Acute Myeloid Leukemia (AML) Blasts Harbor Regulatory Network Proteins Potentially Involved in Antagonism of Apoptosis. Mol Cell Proteomics 2016; 15:1281-98. [PMID: 26801919 DOI: 10.1074/mcp.m115.052944] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Indexed: 12/28/2022] Open
Abstract
Expression of apoptosis-regulating proteins (B-cell CLL/lymphoma 2 - BCL-2, Myeloid Cell Leukemia 1 - MCL-1, BCL-2 like 1 - BCL-X and BCL-2-associated X protein - BAX) in acute myeloid leukemia (AML) blasts at diagnosis is associated with disease-free survival. We previously found that the initially high apoptosis-resistance of AML cells decreased after therapy, while regaining high levels at relapse. Herein, we further explored this aspect of dynamic apoptosis regulation in AML. First, we showed that the intraindividualex vivoapoptosis-related profiles of normal lymphocytes and AML blasts within the bone marrow of AML patients were highly correlated. The expression values of apoptosis-regulating proteins were far beyond healthy control lymphocytes, which implicates the influence of microenvironmental factors. Second, we demonstrated that apoptosis-resistant primary AML blasts, as opposed to apoptosis-sensitive cells, were able to up-regulate BCL-2 expression in sensitive AML blasts in contact cultures (p= 0.0067 andp= 1.0, respectively). Using secretome proteomics, we identified novel proteins possibly engaged in apoptosis regulation. Intriguingly, this analysis revealed that major functional protein clusters engaged in global gene regulation, including mRNA splicing, protein translation, and chromatin remodeling, were more abundant (p= 4.01E-06) in secretomes of apoptosis-resistant AML. These findings were confirmed by subsequent extracellular vesicle proteomics. Finally, confocal-microscopy-based colocalization studies show that splicing factors-containing vesicles secreted by high AAI cells are taken up by low AAI cells. The current results constitute the first comprehensive analysis of proteins released by apoptosis-resistant and sensitive primary AML cells. Together, the data point to vesicle-mediated release of global gene regulatory protein clusters as a plausible novel mechanism of induction of apoptosis resistance. Deciphering the modes of communication between apoptosis-resistant blasts may in perspective lead to the discovery of prognostic tools and development of novel therapeutic interventions, aimed at limiting or overcoming therapy resistance.
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Affiliation(s)
| | | | | | | | - Jaco C Knol
- ¶OncoProteomics Laboratory, Dept. of Medical Oncology
| | - Thang V Pham
- ¶OncoProteomics Laboratory, Dept. of Medical Oncology
| | - Gerrit Jansen
- ‖Dept. of Rheumatology, VUmc-Cancer Center Amsterdam, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - René J P Musters
- **Dept. of Physiology, ICaR-VU, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | | | - Yehuda G Assaraf
- ‡‡Dept. of Biology, Fred Wyszkowski Cancer Research Laboratory, Faculty of Biology, Technion-Israel, Institute of Technology, Haifa 3200003, Israel
| | | | | | - Jacqueline Cloos
- From the ‡Dept. of Pediatric Oncology/Hematology, §Dept. of Hematology
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49
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Madende M, Osthoff G, Patterton HG, Patterton HE, Martin P, Opperman DJ. Characterization of casein and alpha lactalbumin of African elephant (Loxodonta africana) milk. J Dairy Sci 2015; 98:8308-18. [PMID: 26454297 DOI: 10.3168/jds.2014-9195] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 08/14/2015] [Indexed: 11/19/2022]
Abstract
The current research reports partial characterization of the caseins and α-lactalbumin (α-LA) of the African elephant with proposed unique structure-function properties. Extensive research has been carried out to understand the structure of the casein micelles. Crystallographic structure elucidation of caseins and casein micelles is not possible. Consequently, several models have been developed in an effort to describe the casein micelle, specifically of cow milk. Here we report the characterization of African elephant milk caseins. The κ-caseins and β-caseins were investigated, and their relative ratio was found to be approximately 1:8.5, whereas α-caseins were not detected. The gene sequence of β-casein in the NCBI database was revisited, and a different sequence in the N-terminal region is proposed. Amino acid sequence alignment and hydropathy plots showed that the κ-casein of African elephant milk is similar to that of other mammals, whereas the β-casein is similar to the human protein, and displayed a section of unique AA composition and additional hydrophilic regions compared with bovine caseins. Elephant milk is destabilized by 62% alcohol, and it is speculated that the β-casein characteristics may allow maintenance of the colloidal nature of the casein micelle, a role that was previously only associated with κ-casein. The oligosaccharide content of milk was reported to be low in dairy animals but high in some other species such as humans and elephants. In the milk of the African elephant, lactose and oligosaccharides both occur at high levels. These levels are typically related to the content of α-LA in the mammary gland and thus point to a specialized carbohydrate synthesis, where the whey protein α-LA plays a role. We report the characterization of African elephant α-LA. Homology modeling of the α-LA showed that it is structurally similar to crystal structures of other mammalian species, which in turn may be an indication that its functional properties, such as lactose synthesis, should not be impaired.
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Affiliation(s)
- M Madende
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, PO Box 339, Bloemfontein 9300, Republic of South Africa
| | - G Osthoff
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, PO Box 339, Bloemfontein 9300, Republic of South Africa.
| | - H-G Patterton
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, PO Box 339, Bloemfontein 9300, Republic of South Africa
| | - H E Patterton
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, PO Box 339, Bloemfontein 9300, Republic of South Africa
| | - P Martin
- UMR1313 Génétique Animale et Biologie Integrative, Institut National de la Recherche Agronomique, Domaine de Vilvert - Bâtiment 221, 78350 Jouy-en-Josas, France
| | - D J Opperman
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, PO Box 339, Bloemfontein 9300, Republic of South Africa
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Weißer J, Lai ZW, Bronsert P, Kuehs M, Drendel V, Timme S, Kuesters S, Jilg CA, Wellner UF, Lassmann S, Werner M, Biniossek ML, Schilling O. Quantitative proteomic analysis of formalin-fixed, paraffin-embedded clear cell renal cell carcinoma tissue using stable isotopic dimethylation of primary amines. BMC Genomics 2015. [PMID: 26220445 PMCID: PMC4518706 DOI: 10.1186/s12864-015-1768-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background Formalin-fixed, paraffin-embedded (FFPE) tissues represent the most abundant resource of archived human specimens in pathology. Such tissue specimens are emerging as a highly valuable resource for translational proteomic studies. In quantitative proteomic analysis, reductive di-methylation of primary amines using stable isotopic formaldehyde variants is increasingly used due to its robustness and cost-effectiveness. Results In the present study we show for the first time that isotopic amine dimethylation can be used in a straightforward manner for the quantitative proteomic analysis of FFPE specimens without interference from formalin employed in the FFPE process. Isotopic amine dimethylation of FFPE specimens showed equal labeling efficiency as for cryopreserved specimens. For both FFPE and cryopreserved specimens, differential labeling of identical samples yielded highly similar ratio distributions within the expected range for dimethyl labeling. In an initial application, we profiled proteome changes in clear cell renal cell carcinoma (ccRCC) FFPE tissue specimens compared to adjacent non–malignant renal tissue. Our findings highlight increased levels of glyocolytic enzymes, annexins as well as ribosomal and proteasomal proteins. Conclusion Our study establishes isotopic amine dimethylation as a versatile tool for quantitative proteomic analysis of FFPE specimens and underlines proteome alterations in ccRCC. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1768-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- J Weißer
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany. .,Present address: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, A-1090, Vienna, Austria.
| | - Z W Lai
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany.
| | - P Bronsert
- Department of Pathology, University Medical Center Freiburg, Freiburg, Germany. .,Comprehensive Cancer Center Freiburg, Freiburg, Germany. .,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - M Kuehs
- Department of Pathology, University Medical Center Freiburg, Freiburg, Germany.
| | - V Drendel
- Department of Pathology, University Medical Center Freiburg, Freiburg, Germany.
| | - S Timme
- Department of Pathology, University Medical Center Freiburg, Freiburg, Germany.
| | - S Kuesters
- Clinic for General and Visceral Surgery, University Medical Center Freiburg, Freiburg, Germany.
| | - C A Jilg
- Urologische Klinik und Zentrale Klinische Forschung, Klinikum der Universität Freiburg, Freiburg, 79106, Germany.
| | - U F Wellner
- Clinic for General and Visceral Surgery, University Medical Center Freiburg, Freiburg, Germany. .,Present address: Clinic for Surgery, University Clinic of Schleswig-Holstein Campus Lübeck, Lübeck, Germany.
| | - S Lassmann
- Department of Pathology, University Medical Center Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104, Freiburg, Germany. .,Comprehensive Cancer Center Freiburg, Freiburg, Germany. .,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - M Werner
- Department of Pathology, University Medical Center Freiburg, Freiburg, Germany. .,Comprehensive Cancer Center Freiburg, Freiburg, Germany. .,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - M L Biniossek
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany.
| | - O Schilling
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104, Freiburg, Germany. .,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
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