1
|
Sridharan D, Dougherty JA, Ahmed U, Sanghvi SK, Alvi SB, Park KH, Islam H, Knoblaugh SE, Singh H, Kirby ED, Khan M. Bioorthogonal non-canonical amino acid tagging to track transplanted human induced pluripotent stem cell-specific proteome. Stem Cell Res Ther 2024; 15:186. [PMID: 38926849 PMCID: PMC11210150 DOI: 10.1186/s13287-024-03792-3] [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: 01/19/2024] [Accepted: 06/09/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Human induced pluripotent stem cells (hiPSCs) and their differentiated cell types have a great potential for tissue repair and regeneration. While the primary focus of using hiPSCs has historically been to regenerate damaged tissue, emerging studies have shown a more potent effect of hiPSC-derived paracrine factors on tissue regeneration. However, the precise contents of the transplanted hiPSC-derived cell secretome are ambiguous. This is mainly due to the lack of tools to distinguish cell-specific secretome from host-derived proteins in a complex tissue microenvironment in vivo. METHODS In this study, we present the generation and characterization of a novel hiPSC line, L274G-hiPSC, expressing the murine mutant methionyl-tRNA synthetase, L274GMmMetRS, which can be used for tracking the cell specific proteome via biorthogonal non-canonical amino acid tagging (BONCAT). We assessed the trilineage differentiation potential of the L274G-hiPSCs in vitro and in vivo. Furthermore, we assessed the cell-specific proteome labelling in the L274G-hiPSC derived cardiomyocytes (L274G-hiPSC-CMs) in vitro following co-culture with wild type human umbilical vein derived endothelial cells and in vivo post transplantation in murine hearts. RESULTS We demonstrated that the L274G-hiPSCs exhibit typical hiPSC characteristics and that we can efficiently track the cell-specific proteome in their differentiated progenies belonging to the three germ lineages, including L274G-hiPSC-CMs. Finally, we demonstrated cell-specific BONCAT in transplanted L274G-hiPSC-CMs. CONCLUSION The novel L274G-hiPSC line can be used to study the cell-specific proteome of hiPSCs in vitro and in vivo, to delineate mechanisms underlying hiPSC-based cell therapies for a variety of regenerative medicine applications.
Collapse
Affiliation(s)
- Divya Sridharan
- Division of Basic and Translational Sciences, Department of Emergency Medicine, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Julie A Dougherty
- Division of Basic and Translational Sciences, Department of Emergency Medicine, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Uzair Ahmed
- Division of Basic and Translational Sciences, Department of Emergency Medicine, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Shridhar K Sanghvi
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, USA
- Department of Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH, USA
| | - Syed Baseeruddin Alvi
- Division of Basic and Translational Sciences, Department of Emergency Medicine, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Ki Ho Park
- Department of Surgery, University of Virginia, Charlottesville, VA, USA
| | - Helena Islam
- Division of Basic and Translational Sciences, Department of Emergency Medicine, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Sue E Knoblaugh
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - Harpreet Singh
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, USA
| | - Elizabeth D Kirby
- Department of Psychology, The Ohio State University, Columbus, OH, USA
- Chronic Brain Injury Program, The Ohio State University, Columbus, OH, USA
| | - Mahmood Khan
- Division of Basic and Translational Sciences, Department of Emergency Medicine, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
2
|
Ehlers SF, Manikowski D, Steffes G, Ehring K, Gude F, Grobe K. A Residual N-Terminal Peptide Enhances Signaling of Depalmitoylated Hedgehog to the Patched Receptor. J Dev Biol 2024; 12:11. [PMID: 38651456 PMCID: PMC11036296 DOI: 10.3390/jdb12020011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 03/26/2024] [Accepted: 04/07/2024] [Indexed: 04/25/2024] Open
Abstract
During their biosynthesis, Sonic hedgehog (Shh) morphogens are covalently modified by cholesterol at the C-terminus and palmitate at the N-terminus. Although both lipids initially anchor Shh to the plasma membrane of producing cells, it later translocates to the extracellular compartment to direct developmental fates in cells expressing the Patched (Ptch) receptor. Possible release mechanisms for dually lipidated Hh/Shh into the extracellular compartment are currently under intense debate. In this paper, we describe the serum-dependent conversion of the dually lipidated cellular precursor into a soluble cholesteroylated variant (ShhC) during its release. Although ShhC is formed in a Dispatched- and Scube2-dependent manner, suggesting the physiological relevance of the protein, the depalmitoylation of ShhC during release is inconsistent with the previously postulated function of N-palmitate in Ptch receptor binding and signaling. Therefore, we analyzed the potency of ShhC to induce Ptch-controlled target cell transcription and differentiation in Hh-sensitive reporter cells and in the Drosophila eye. In both experimental systems, we found that ShhC was highly bioactive despite the absence of the N-palmitate. We also found that the artificial removal of N-terminal peptides longer than eight amino acids inactivated the depalmitoylated soluble proteins in vitro and in the developing Drosophila eye. These results demonstrate that N-depalmitoylated ShhC requires an N-peptide of a defined minimum length for its signaling function to Ptch.
Collapse
Affiliation(s)
- Sophia F. Ehlers
- Institute of Physiological Chemistry and Pathobiochemistry, Faculty of Medicine, University of Münster, Waldeyerstrasse 15, 48149 Münster, Germany; (S.F.E.); (D.M.); (K.E.); (F.G.)
| | - Dominique Manikowski
- Institute of Physiological Chemistry and Pathobiochemistry, Faculty of Medicine, University of Münster, Waldeyerstrasse 15, 48149 Münster, Germany; (S.F.E.); (D.M.); (K.E.); (F.G.)
| | - Georg Steffes
- Institute for Neuro- and Behavioral Biology, Faculty of Biology, University of Münster, Röntgenstrasse 16, 48149 Münster, Germany;
| | - Kristina Ehring
- Institute of Physiological Chemistry and Pathobiochemistry, Faculty of Medicine, University of Münster, Waldeyerstrasse 15, 48149 Münster, Germany; (S.F.E.); (D.M.); (K.E.); (F.G.)
| | - Fabian Gude
- Institute of Physiological Chemistry and Pathobiochemistry, Faculty of Medicine, University of Münster, Waldeyerstrasse 15, 48149 Münster, Germany; (S.F.E.); (D.M.); (K.E.); (F.G.)
| | - Kay Grobe
- Institute of Physiological Chemistry and Pathobiochemistry, Faculty of Medicine, University of Münster, Waldeyerstrasse 15, 48149 Münster, Germany; (S.F.E.); (D.M.); (K.E.); (F.G.)
| |
Collapse
|
3
|
Luu JK, Johnson FD, Jajarmi J, Sihota T, Shi R, Lu D, Farnsworth D, Spencer SE, Negri GL, Morin GB, Lockwood WW. Characterizing the secretome of EGFR mutant lung adenocarcinoma. Front Oncol 2024; 13:1286821. [PMID: 38260835 PMCID: PMC10801028 DOI: 10.3389/fonc.2023.1286821] [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: 08/31/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024] Open
Abstract
Background Lung cancer is the leading cause of cancer related death worldwide, mainly due to the late stage of disease at the time of diagnosis. Non-invasive biomarkers are needed to supplement existing screening methods to enable earlier detection and increased patient survival. This is critical to EGFR-driven lung adenocarcinoma as it commonly occurs in individuals who have never smoked and do not qualify for current screening protocols. Methods In this study, we performed mass spectrometry analysis of the secretome of cultured lung cells representing different stages of mutant EGFR driven transformation, from normal to fully malignant. Identified secreted proteins specific to the malignant state were validated using orthogonal methods and their clinical activity assessed in lung adenocarcinoma patient cohorts. Results We quantified 1020 secreted proteins, which were compared for differential expression between stages of transformation. We validated differentially expressed proteins at the transcriptional level in clinical tumor specimens, association with patient survival, and absolute concentration to yield three biomarker candidates: MDK, GDF15, and SPINT2. These candidates were validated using ELISA and increased levels were associated with poor patient survival specifically in EGFR mutant lung adenocarcinoma patients. Conclusions Our study provides insight into changes in secreted proteins during EGFR driven lung adenocarcinoma transformation that may play a role in the processes that promote tumor progression. The specific candidates identified can harnessed for biomarker use to identify high risk individuals for early detection screening programs and disease management for this molecular subgroup of lung adenocarcinoma patients.
Collapse
Affiliation(s)
- Jennifer K. Luu
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Fraser D. Johnson
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Jana Jajarmi
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Tianna Sihota
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Rocky Shi
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Daniel Lu
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Dylan Farnsworth
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Sandra E. Spencer
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Gian Luca Negri
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Gregg B. Morin
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - William W. Lockwood
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia (UBC), Vancouver, BC, Canada
| |
Collapse
|
4
|
Wu W, Krijgsveld J. Secretome Analysis: Reading Cellular Sign Language to Understand Intercellular Communication. Mol Cell Proteomics 2024; 23:100692. [PMID: 38081362 PMCID: PMC10793180 DOI: 10.1016/j.mcpro.2023.100692] [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: 08/07/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 01/06/2024] Open
Abstract
A significant portion of mammalian proteomes is secreted to the extracellular space to fulfill crucial roles in cell-to-cell communication. To best recapitulate the intricate and multi-faceted crosstalk between cells in a live organism, there is an ever-increasing need for methods to study protein secretion in model systems that include multiple cell types. In addition, posttranslational modifications further expand the complexity and versatility of cellular communication. This review aims to summarize recent strategies and model systems that employ cellular coculture, chemical biology tools, protein enrichment, and proteomic methods to characterize the composition and function of cellular secretomes. This is all geared towards gaining better understanding of organismal biology in vivo mediated by secretory signaling.
Collapse
Affiliation(s)
- Wei Wu
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore; Department of Pharmacy, National University of Singapore, Singapore, Singapore.
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany; Medical Faculty, Heidelberg University, Heidelberg, Germany.
| |
Collapse
|
5
|
Burgess JD, Amerna D, Norton ES, Parsons TM, Perkerson RB, Faroqi AH, Wszolek ZK, Guerrero Cazares H, Kanekiyo T, Delenclos M, McLean PJ. A mutant methionyl-tRNA synthetase-based toolkit to assess induced-mesenchymal stromal cell secretome in mixed-culture disease models. Stem Cell Res Ther 2023; 14:289. [PMID: 37798772 PMCID: PMC10557244 DOI: 10.1186/s13287-023-03515-0] [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: 04/20/2023] [Accepted: 09/25/2023] [Indexed: 10/07/2023] Open
Abstract
BACKGROUND Mesenchymal stromal cells (MSCs) have a dynamic secretome that plays a critical role in tissue repair and regeneration. However, studying the MSC secretome in mixed-culture disease models remains challenging. This study aimed to develop a mutant methionyl-tRNA synthetase-based toolkit (MetRSL274G) to selectively profile secreted proteins from MSCs in mixed-culture systems and demonstrate its potential for investigating MSC responses to pathological stimulation. METHODS We used CRISPR/Cas9 homology-directed repair to stably integrate MetRSL274G into cells, enabling the incorporation of the non-canonical amino acid, azidonorleucine (ANL), and facilitating selective protein isolation using click chemistry. MetRSL274G was integrated into both in H4 cells and induced pluripotent stem cells (iPSCs) for a series of proof-of-concept studies. Following iPSC differentiation into induced-MSCs, we validated their identity and co-cultured MetRSL274G-expressing iMSCs with naïve or lipopolysaccharide (LPS)-treated THP-1 cells. We then profiled the iMSC secretome using antibody arrays. RESULTS Our results showed successful integration of MetRSL274G into targeted cells, allowing specific isolation of proteins from mixed-culture environments. We also demonstrated that the secretome of MetRSL274G-expressing iMSCs can be differentiated from that of THP-1 cells in co-culture and is altered when co-cultured with LPS-treated THP-1 cells compared to naïve THP-1 cells. CONCLUSIONS The MetRSL274G-based toolkit we have generated enables selective profiling of the MSC secretome in mixed-culture disease models. This approach has broad applications for examining not only MSC responses to models of pathological conditions, but any other cell type that can be differentiated from iPSCs. This can potentially reveal novel MSC-mediated repair mechanisms and advancing our understanding of tissue regeneration processes.
Collapse
Affiliation(s)
- Jeremy D Burgess
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, USA
- Regenerative Sciences Training Program, Center for Regenerative Medicine, Mayo Clinic, Jacksonville, FL, USA
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Danilyn Amerna
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Emily S Norton
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, USA
- Regenerative Sciences Training Program, Center for Regenerative Medicine, Mayo Clinic, Jacksonville, FL, USA
- Department of Neurosurgery, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Tammee M Parsons
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Ralph B Perkerson
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Ayman H Faroqi
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, USA
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Zbigniew K Wszolek
- Department of Neurology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Hugo Guerrero Cazares
- Department of Neurosurgery, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Takahisa Kanekiyo
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Marion Delenclos
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Pamela J McLean
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.
| |
Collapse
|
6
|
Knecht S, Eberl HC, Kreisz N, Ugwu UJ, Starikova T, Kuster B, Wilhelm S. An Introduction to Analytical Challenges, Approaches, and Applications in Mass Spectrometry-Based Secretomics. Mol Cell Proteomics 2023; 22:100636. [PMID: 37597723 PMCID: PMC10518356 DOI: 10.1016/j.mcpro.2023.100636] [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: 02/27/2023] [Revised: 07/06/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023] Open
Abstract
The active release of proteins into the extracellular space and the proteolytic cleavage of cell surface proteins are key processes that coordinate and fine-tune a multitude of physiological functions. The entirety of proteins that fulfill these extracellular tasks are referred to as the secretome and are of special interest for the investigation of biomarkers of disease states and physiological processes related to cell-cell communication. LC-MS-based proteomics approaches are a valuable tool for the comprehensive and unbiased characterization of this important subproteome. This review discusses procedures, opportunities, and limitations of mass spectrometry-based secretomics to better understand and navigate the complex analytical landscape for studying protein secretion in biomedical science.
Collapse
Affiliation(s)
- Sascha Knecht
- Omics Sciences, Genomic Sciences, GlaxoSmithKline, Heidelberg, Germany; Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - H Christian Eberl
- Omics Sciences, Genomic Sciences, GlaxoSmithKline, Heidelberg, Germany
| | - Norbert Kreisz
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Ukamaka Juliet Ugwu
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Tatiana Starikova
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
| | - Stephanie Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
| |
Collapse
|
7
|
Hajisoltani R, Taghizadeh M, Hamblin MR, Ramezani F. Could conditioned medium be used instead of stem cell transplantation to repair spinal cord injury in animal models? Identifying knowledge gaps. J Neuropathol Exp Neurol 2023; 82:753-759. [PMID: 37535839 DOI: 10.1093/jnen/nlad053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023] Open
Abstract
The drawbacks of stem cell (SC) therapies have led to investigations of SC conditioned medium (CM) instead of SC transplantation in the repair of spinal cord injury (SCI). However, the effectiveness of CM in comparison with cell transplantation in SCI models remain an open and intriguing question. The focus of this review was to survey existing publications addressing this comparison. The review included articles from electronic databases Medline, Embase, Scopus, and Web of Science that included comparisons of the effects of CM versus SC transplantation and versus controls on locomotion after SCI. The search yielded 5 studies and 6 experiments. The results indicated that there was insufficient evidence to conclude that treatment with CM and source cells were equally effective (SMD = 0.12; 95% CI = -0.36 to 0.59; p = 0.07). Regarding investigations of separate effects of SCs versus CM, there currently is limited evidence on efficacy in SCI models. This highlights a notable concern affecting this field. Thus, we identified critical knowledge gaps concerning comparisons of the efficacy of therapeutic application of SC and their derived CM on functional recovery following SCI.
Collapse
Affiliation(s)
- Razieh Hajisoltani
- Physiology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mona Taghizadeh
- Physiology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, South Africa
| | - Fatemeh Ramezani
- Physiology Research Center, Iran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
8
|
Kirschner F, Arnold-Schild D, Leps C, Łącki MK, Klein M, Chen Y, Ludt A, Marini F, Kücük C, Stein L, Distler U, Sielaff M, Michna T, Riegel K, Rajalingam K, Bopp T, Tenzer S, Schild H. Modulation of cellular transcriptome and proteome composition by azidohomoalanine-implications on click chemistry-based secretome analysis. J Mol Med (Berl) 2023; 101:855-867. [PMID: 37231147 PMCID: PMC10300158 DOI: 10.1007/s00109-023-02333-4] [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: 02/24/2023] [Revised: 04/25/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
The analysis of the secretome provides important information on proteins defining intercellular communication and the recruitment and behavior of cells in specific tissues. Especially in the context of tumors, secretome data can support decisions for diagnosis and therapy. The mass spectrometry-based analysis of cell-conditioned media is widely used for the unbiased characterization of cancer secretomes in vitro. Metabolic labeling using azide-containing amino acid analogs in combination with click chemistry facilitates this type of analysis in the presence of serum, preventing serum starvation-induced effects. The modified amino acid analogs, however, are less efficiently incorporated into newly synthesized proteins and may perturb protein folding. Combining transcriptome and proteome analysis, we elucidate in detail the effects of metabolic labeling with the methionine analog azidohomoalanine (AHA) on gene and protein expression. Our data reveal that 15-39% of the proteins detected in the secretome displayed changes in transcript and protein expression induced by AHA labeling. Gene Ontology (GO) analyses indicate that metabolic labeling using AHA leads to induction of cellular stress and apoptosis-related pathways and provide first insights on how this affects the composition of the secretome on a global scale. KEY MESSAGES: Azide-containing amino acid analogs affect gene expression profiles. Azide-containing amino acid analogs influence cellular proteome. Azidohomoalanine labeling induces cellular stress and apoptotic pathways. Secretome consists of proteins with dysregulated expression profiles.
Collapse
Affiliation(s)
- Friederike Kirschner
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Danielle Arnold-Schild
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Christian Leps
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Mateusz Krzysztof Łącki
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Matthias Klein
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Yannic Chen
- Helmholtz Institute Translational Oncology, Obere Zahlbacher Straße 63, 55131, Mainz, Germany
| | - Annekathrin Ludt
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Can Kücük
- Helmholtz Institute Translational Oncology, Obere Zahlbacher Straße 63, 55131, Mainz, Germany
| | - Lara Stein
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Ute Distler
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Malte Sielaff
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Thomas Michna
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Kristina Riegel
- Cell Biology Unit, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Krishnaraj Rajalingam
- Cell Biology Unit, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Tobias Bopp
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- University Cancer Center Mainz, Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- German Cancer Consortium (DKTK), Mainz, Germany
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany.
- Helmholtz Institute Translational Oncology, Obere Zahlbacher Straße 63, 55131, Mainz, Germany.
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
| | - Hansjörg Schild
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany.
- Helmholtz Institute Translational Oncology, Obere Zahlbacher Straße 63, 55131, Mainz, Germany.
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
- University Cancer Center Mainz, Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
| |
Collapse
|
9
|
Silveira BM, Ribeiro TO, Freitas RS, Carreira ACO, Gonçalves MS, Sogayar M, Meyer R, Birbrair A, Fortuna V. Secretome from human adipose-derived mesenchymal stem cells promotes blood vessel formation and pericyte coverage in experimental skin repair. PLoS One 2022; 17:e0277863. [PMID: 36534643 PMCID: PMC9762598 DOI: 10.1371/journal.pone.0277863] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/04/2022] [Indexed: 12/24/2022] Open
Abstract
Human adipose tissue-derived stem cells (hASC) secretome display various therapeutically relevant effects in regenerative medicine, such as induction of angiogenesis and tissue repair. The benefits of hASC secretome are primarily orchestrated by trophic factors that mediate autocrine and paracrine effects in host cells. However, the composition and the innate characteristics of hASC secretome can be highly variable depending on the culture conditions. Here, we evaluated the combined effect of serum-free media and hypoxia preconditioning on the hASCs secretome composition and biological effects on angiogenesis and wound healing. The hASCs were cultured in serum-free media under normoxic (NCM) or hypoxic (HCM) preconditioning. The proteomic profile showed that pro- and anti-antiangiogenic factors were detected in NCM and HCM secretomes. In vitro studies demonstrated that hASCs secretomes enhanced endothelial proliferation, survival, migration, in vitro tube formation, and in vivo Matrigel plug angiogenesis. In a full-thickness skin-wound mouse model, injection of either NCM or HCM significantly accelerated the wound healing. Finally, hASC secretomes were potent in increasing endothelial density and vascular coverage of resident pericytes expressing NG2 and nestin to the lesion site, potentially contributing to blood vessel maturation. Overall, our data suggest that serum-free media or hypoxic preconditioning enhances the vascular regenerative effects of hASC secretome in a preclinical wound healing model.
Collapse
Affiliation(s)
- Brysa M. Silveira
- Health Science Institute, Federal University of Bahia, Salvador, BA, Brazil
| | - Tiago O. Ribeiro
- Health Science Institute, Federal University of Bahia, Salvador, BA, Brazil
| | - Railane S. Freitas
- Health Science Institute, Federal University of Bahia, Salvador, BA, Brazil
| | - Ana C. O. Carreira
- Department of Surgery, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Marilda Souza Gonçalves
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, BA, Brazil
- Department of Clinical Analysis, Faculty of Pharmacy, Federal University of Bahia, Salvador, BA, Brazil
| | - Mari Sogayar
- Cell and Molecular Therapy Center (NUCEL), Medical School, University of São Paulo, São Paulo, Brazil
- Biochemistry Department, Chemistry Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Roberto Meyer
- Health Science Institute, Federal University of Bahia, Salvador, BA, Brazil
| | - Alexander Birbrair
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
- Department of Radiology, Columbia University Medical Center, New York, NY, United States of America
- Department of Dermatology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Vitor Fortuna
- Health Science Institute, Federal University of Bahia, Salvador, BA, Brazil
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, BA, Brazil
- * E-mail:
| |
Collapse
|
10
|
Soluble ANPEP Released From Human Astrocytes as a Positive Regulator of Microglial Activation and Neuroinflammation: Brain Renin-Angiotensin System in Astrocyte-Microglia Crosstalk. Mol Cell Proteomics 2022; 21:100424. [PMID: 36220603 PMCID: PMC9650055 DOI: 10.1016/j.mcpro.2022.100424] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 10/01/2022] [Accepted: 10/05/2022] [Indexed: 11/07/2022] Open
Abstract
Astrocytes are major supportive glia and immune modulators in the brain; they are highly secretory in nature and interact with other cell types via their secreted proteomes. To understand how astrocytes communicate during neuroinflammation, we profiled the secretome of human astrocytes following stimulation with proinflammatory factors. A total of 149 proteins were significantly upregulated in stimulated astrocytes, and a bioinformatics analysis of the astrocyte secretome revealed that the brain renin-angiotensin system (RAS) is an important mechanism of astrocyte communication. We observed that the levels of soluble form of aminopeptidase N (sANPEP), an RAS component that converts angiotensin (Ang) III to Ang IV in a neuroinflammatory milieu, significantly increased in the astrocyte secretome. To elucidate the role of sANPEP and Ang IV in neuroinflammation, we first evaluated the expression of Ang IV receptors in human glial cells because Ang IV mediates biological effects through its receptors. The expression of angiotensin type 1 receptor was considerably upregulated in activated human microglial cells but not in human astrocytes. Moreover, interleukin-1β release from human microglial cells was synergistically increased by cotreatment with sANPEP and its substrate, Ang III, suggesting the proinflammatory action of Ang IV generated by sANPEP. In a mouse neuroinflammation model, brain microglial activation and proinflammatory cytokine expression levels were increased by intracerebroventricular injection of sANPEP and attenuated by an enzymatic inhibitor and neutralizing antibody against sANPEP. Collectively, our results indicate that astrocytic sANPEP-induced increase in Ang IV exacerbates neuroinflammation by interacting with microglial proinflammatory receptor angiotensin type 1 receptor, highlighting an important role of indirect crosstalk between astrocytes and microglia through the brain RAS in neuroinflammation.
Collapse
|
11
|
Decoene I, Herpelinck T, Geris L, Luyten FP, Papantoniou I. Engineering bone-forming callus organoid implants in a xenogeneic-free differentiation medium. FRONTIERS IN CHEMICAL ENGINEERING 2022. [DOI: 10.3389/fceng.2022.892190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The field of tissue engineering aspires to provide clinically relevant solutions for patients through the integration of developmental engineering principles with a bottom-up manufacturing approach. However, the manufacturing of cell-based advanced therapy medicinal products is hampered by protocol complexity, lack of non-invasive critical quality controls, and dependency on animal-derived components for tissue differentiation. We investigate a serum-free, chemically defined, xeno- and lipid-free chondrogenic differentiation medium to generate bone-forming callus organoids. Our results show an increase in microtissue homogeneity during prolonged differentiation and the high quality of in vivo bone-forming organoids. The low protein content of the culture medium potentially allows for the monitoring of relevant secreted biomarkers as (critical) quality attributes. Together, we envisage that this xeno- and lipid-free chondrogenic medium is compatible with industrial scale-up and automation while facilitating the implementation of non-invasive imaging and the use of quality control parameters based on secreted biomarkers.
Collapse
|
12
|
Sacnun JM, Herzog R, Kratochwill K. Proteomic study of mesothelial and endothelial cross-talk: key lessons. Expert Rev Proteomics 2022; 19:289-296. [PMID: 36714918 DOI: 10.1080/14789450.2023.2174851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
INTRODUCTION The peritoneum, pleura, and pericardium are yet understudied multicellular systems where mesothelial cells (MCs) and endothelial cells (ECs) are in close proximity. Crosstalk between these cell types likely plays role in molecular transport, immunological reactions, and metabolic processes in health, disease, and therapeutic intervention. AREAS COVERED In this review, we discuss recent proteomic efforts to characterize the crosstalk between MC and EC. We describe the proteomic methods necessary for investigation of crosstalk between MC and EC, as well as the in-vitro models that can be employed. Potential experimental approaches range from conditioned medium, via co-culture on semi-permeable membranes, to 3D cell culture based organoid models. While the biological and clinical relevance of the models may increase with their ability to mimic close cell communication, the practicality of these complex experiments corresponds vice versa, making standardization more difficult and expensive. EXPERT OPINION Currently, data and reports on mesothelial-to-endothelial crosstalk are still very scarce. In our opinion, the in-vitro model using semi-permeable cell culture inserts will allow to establish a basic understanding of cellular crosstalk that may occur between those cell types. Later-on, more sophisticated 3D cell cultures may be better able to simulate the transport dynamics within the peritoneal membrane.
Collapse
Affiliation(s)
- Juan Manuel Sacnun
- Christian Doppler Laboratory for Molecular Stress Research in Peritoneal Dialysis, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria.,Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Rebecca Herzog
- Christian Doppler Laboratory for Molecular Stress Research in Peritoneal Dialysis, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria.,Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Klaus Kratochwill
- Christian Doppler Laboratory for Molecular Stress Research in Peritoneal Dialysis, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria.,Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| |
Collapse
|
13
|
Khanefard N, Sapavee S, Akeprathumchai S, Mekvichitsaeng P, Poomputsa K. Production of Neuraminidase Virus Like Particles by Stably Transformed Insect Cells: A Simple Process for NA-Based Influenza Vaccine Development. Mol Biotechnol 2022; 64:1409-1418. [PMID: 35704162 PMCID: PMC9198613 DOI: 10.1007/s12033-022-00519-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/30/2022] [Indexed: 11/28/2022]
Abstract
Neuraminidase (NA) is a second major surface protein of the influenza virus and has recently been suggested as a supplemental antigen to the major immunodominant hemagglutinin (HA) antigen in the influenza vaccine. NA is less affected by antigenic drift compared to the HA, induces strong anti-neuraminidase immune responses, and provides broader protection against many influenza strains. However, the NA amount in currently licensed influenza virus vaccines is much lower than that of HA, and not standardized. A platform to produce NA antigen, in the form of virus-like particles (VLPs), was thus developed, to facilitate supplementation of NA antigen in the influenza vaccine formula. Stably transformed Sf9 insect cells had been engineered to express the influenza A virus (H5N1) NA gene under a baculovirus OpMNPV IE2 promoter. Recombinant NA protein was synthesized and assembled into VLPs, in the intact cellular environment provided by insect cells. Approximately 150 µg/ml of NA-VLPs was obtained in the culture medium. Purification of the NA-VLPs was achieved by a sucrose density gradient ultracentrifugation. The purified NA-VLPs effectively induced anti-NA antibodies with neuraminidase inhibition activities in mice. This work demonstrates a simple process to produce an immunocompetent NA-VLPs antigen, exclusively made of only neuraminidase, by insect cells.
Collapse
Affiliation(s)
- Najmeh Khanefard
- Biotechnology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bangkhunthian), Bangkok, 10150, Thailand
| | - Saithip Sapavee
- Biotechnology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bangkhunthian), Bangkok, 10150, Thailand
| | - Saengchai Akeprathumchai
- Biotechnology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bangkhunthian), Bangkok, 10150, Thailand
| | - Phenjun Mekvichitsaeng
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (Bangkhunthian), Bangkok, 10150, Thailand
| | - Kanokwan Poomputsa
- Biotechnology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bangkhunthian), Bangkok, 10150, Thailand.
| |
Collapse
|
14
|
Shin S, Lee S, Choi S, Park N, Kwon Y, Jeong J, Ju S, Chang Y, Park K, Ha C, Lee C. Characterization of the Secretome of a Specific Cell Expressing Mutant Methionyl-tRNA Synthetase in Co-Culture Using Click Chemistry. Int J Mol Sci 2022; 23:ijms23126527. [PMID: 35742968 PMCID: PMC9223471 DOI: 10.3390/ijms23126527] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 11/21/2022] Open
Abstract
Co-culture system, in which two or more distinct cell types are cultured together, is advantageous in that it can mimic the environment of the in vivo niche of the cells. In this study, we presented a strategy to analyze the secretome of a specific cell type under the co-culture condition in serum-supplemented media. For the cell-specific secretome analysis, we expressed the mouse mutant methionyl-tRNA synthetase for the incorporation of the non-canonical amino acid, azidonorleucine into the newly synthesized proteins in cells of which the secretome is targeted. The azidonorleucine-tagged secretome could be enriched, based on click chemistry, and distinguished from any other contaminating proteins, either from the cell culture media or the other cells co-cultured with the cells of interest. In order to have more reliable true-positive identifications of cell-specific secretory bodies, we established criteria to exclude any identified human peptide matched to bovine proteins. As a result, we identified a maximum of 719 secreted proteins in the secretome analysis under this co-culture condition. Last, we applied this platform to profile the secretome of mesenchymal stem cells and predicted its therapeutic potential on osteoarthritis based on secretome analysis.
Collapse
Affiliation(s)
- Sungho Shin
- Chemical & Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea; (S.S.); (S.L.); (N.P.); (Y.K.); (S.J.)
- KHU-KIST Department of Converging Science and Technology, Graduate School, Kyung Hee University, Seoul 02447, Korea;
| | - Seonjeong Lee
- Chemical & Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea; (S.S.); (S.L.); (N.P.); (Y.K.); (S.J.)
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
| | - Sunyoung Choi
- Department of Orthopedic Surgery, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul 06351, Korea; (S.C.); (C.H.)
- Cell and Gene Therapy Institute, Samsung Medical Center, Seoul 06351, Korea;
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06351, Korea
| | - Narae Park
- Chemical & Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea; (S.S.); (S.L.); (N.P.); (Y.K.); (S.J.)
- KHU-KIST Department of Converging Science and Technology, Graduate School, Kyung Hee University, Seoul 02447, Korea;
| | - Yumi Kwon
- Chemical & Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea; (S.S.); (S.L.); (N.P.); (Y.K.); (S.J.)
| | - Jaehoon Jeong
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul 01812, Korea;
| | - Shinyeong Ju
- Chemical & Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea; (S.S.); (S.L.); (N.P.); (Y.K.); (S.J.)
| | - Yunsil Chang
- Cell and Gene Therapy Institute, Samsung Medical Center, Seoul 06351, Korea;
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06351, Korea
- Department of Pediatrics, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul 06351, Korea
| | - Kangsik Park
- KHU-KIST Department of Converging Science and Technology, Graduate School, Kyung Hee University, Seoul 02447, Korea;
- Department of Physiology, School of Medicine, Kyung Hee University, Seoul 02447, Korea
| | - Chulwon Ha
- Department of Orthopedic Surgery, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul 06351, Korea; (S.C.); (C.H.)
- Cell and Gene Therapy Institute, Samsung Medical Center, Seoul 06351, Korea;
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06351, Korea
| | - Cheolju Lee
- Chemical & Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea; (S.S.); (S.L.); (N.P.); (Y.K.); (S.J.)
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
- Correspondence:
| |
Collapse
|
15
|
Gaurivaud P, Tardy F. The Mycoplasma spp. ‘Releasome’: A New Concept for a Long-Known Phenomenon. Front Microbiol 2022; 13:853440. [PMID: 35495700 PMCID: PMC9051441 DOI: 10.3389/fmicb.2022.853440] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
The bacterial secretome comprises polypeptides expressed at the cell surface or released into the extracellular environment as well as the corresponding secretion machineries. Despite their reduced coding capacities, Mycoplasma spp. are able to produce and release several components into their environment, including polypeptides, exopolysaccharides and extracellular vesicles. Technical difficulties in purifying these elements from the complex broth media used to grow mycoplasmas have recently been overcome by optimizing growth conditions and switching to chemically defined culture media. However, the secretion pathways responsible for the release of these structurally varied elements are still poorly described in mycoplasmas. We propose the use of the term ‘releasome,’ instead of secretome, to refer to molecules released by mycoplasmas into their environment. The aim of this review is to more precisely delineate the elements that should be considered part of the mycoplasmal releasome and their role in the interplay of mycoplasmas with host cells and tissues.
Collapse
|
16
|
Lorenz M, Witt E, Völker U, Stangl K, Stangl V, Hammer E. Serum starvation induces sexual dimorphisms in secreted proteins of human umbilical vein endothelial cells (HUVECs) from twin pairs. Proteomics 2022; 22:e2100168. [PMID: 35357760 DOI: 10.1002/pmic.202100168] [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: 07/21/2021] [Revised: 03/24/2022] [Accepted: 03/24/2022] [Indexed: 11/06/2022]
Abstract
There is growing evidence for sex and gender differences in the clinical manifestation and outcomes of human diseases. Human primary endothelial cells represent a useful cardiovascular model to study sexual dimorphisms at the cellular level. Here, we analyzed sexual dimorphisms of the secretome after serum starvation using HUVECs from twin pairs of the opposite sex to minimize the impact of varying genetic background. HUVECs were starved for 5 and 16 h, respectively, and proteins of the cell culture supernatants were analyzed by tandem mass spectrometry. Altogether, 960 extracellular proteins were identified of which 683 were amendable to stringent quantification. Significant alterations were observed for 324 proteins between long-term and short-term starvation and the majority were similar in both sexes. Only 5 proteins showed significant sex-specific regulation between long- versus short-term starvation. Furthermore, 19 unique proteins with significant sexual dimorphisms at the same time points of serum starvation were observed. A larger number of proteins, e.g. tissue factor inhibitor 2 (TFPI2), displayed higher levels in the supernatants of females compared to male cells after long term serum starvation that might point to higher adaptation capacity of female cells. The overall results demonstrate that male and female cells differ in their secretome. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Mario Lorenz
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Medizinische Klinik für Kardiologie und Angiologie, Campus Mitte, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Berlin
| | - Eric Witt
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Greifswald
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Greifswald
| | - Karl Stangl
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Medizinische Klinik für Kardiologie und Angiologie, Campus Mitte, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Berlin
| | - Verena Stangl
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Medizinische Klinik für Kardiologie und Angiologie, Campus Mitte, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Berlin
| | - Elke Hammer
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Greifswald
| |
Collapse
|
17
|
Kern M, Ferreira-Cerca S. Differential Translation Activity Analysis Using Bioorthogonal Noncanonical Amino Acid Tagging (BONCAT) in Archaea. Methods Mol Biol 2022; 2533:229-246. [PMID: 35796992 PMCID: PMC9761519 DOI: 10.1007/978-1-0716-2501-9_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The study of protein production and degradation in a quantitative and time-dependent manner is a major challenge to better understand cellular physiological response. Among available technologies bioorthogonal noncanonical amino acid tagging (BONCAT) is an efficient approach allowing for time-dependent labeling of proteins through the incorporation of chemically reactive noncanonical amino acids like L-azidohomoalanine (L-AHA). The azide-containing amino-acid derivative enables a highly efficient and specific reaction termed click chemistry, whereby the azide group of the L-AHA reacts with a reactive alkyne derivate, like dibenzocyclooctyne (DBCO) derivatives, using strain-promoted alkyne-azide cycloaddition (SPAAC). Moreover, available DBCO containing reagents are versatile and can be coupled to fluorophore (e.g., Cy7) or affinity tag (e.g., biotin) derivatives, for easy visualization and affinity purification, respectively.Here, we describe a step-by-step BONCAT protocol optimized for the model archaeon Haloferax volcanii , but which is also suitable to harness other biological systems. Finally, we also describe examples of downstream visualization, affinity purification of L-AHA-labeled proteins and differential expression analysis.In conclusion, the following BONCAT protocol expands the available toolkit to explore proteostasis using time-resolved semiquantitative proteomic analysis in archaea .
Collapse
Affiliation(s)
- Michael Kern
- Biochemistry III-Regensburg Center for Biochemistry-Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| | - Sébastien Ferreira-Cerca
- Biochemistry III-Regensburg Center for Biochemistry-Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany.
| |
Collapse
|
18
|
Vargas-Diaz D, Altelaar M. Automated High-Throughput Method for the Fast, Robust, and Reproducible Enrichment of Newly Synthesized Proteins. J Proteome Res 2021; 21:189-199. [PMID: 34860524 PMCID: PMC8749957 DOI: 10.1021/acs.jproteome.1c00743] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
A high-throughput
method was developed for the automated enrichment
of newly synthesized proteins (NSPs), which are labeled metabolically
by substituting methionine with the “click-able” analogue
azidohomoalanine (AHA). A suitable conjugate containing a dibenzocyclooctyne
(DBCO) group allows the specific selection of NSPs by a fast 1 h click
chemistry-based reaction with AHA. Through an automated pipetting
platform, the samples are loaded into streptavidin cartridges for
the selective binding of the NSPs by means of a biotin bait contained
in the conjugate. The enriched proteins are eluted by a reproducible
chemical cleavage of the 4,4-dimethyl-2,6-dioxocyclohexylidene (Dde)
group in the conjugate, which increases selectivity. The NSPs can
be collected and digested in the same well plate, and the resulting
peptides can be subsequently loaded for automated cleanup, followed
by mass spectrometry analysis. The proposed automated method allows
for the robust and effective enrichment of samples in 96-well plates
in a period of 3 h. Our developed enrichment method was comprehensively
evaluated and then applied to the proteomics analysis of the melanoma
A375 cell secretome, after treatment with the cytokines interferon
α (IFN-α) and γ (IFN-γ), resulting in the
quantification of 283 and 263 proteins, respectively, revealing intricate
tumor growth-supportive and -suppressive effects.
Collapse
Affiliation(s)
- David Vargas-Diaz
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
19
|
Cho JH, Ju WS, Seo SY, Kim BH, Kim JS, Kim JG, Park SJ, Choo YK. The Potential Role of Human NME1 in Neuronal Differentiation of Porcine Mesenchymal Stem Cells: Application of NB-hNME1 as a Human NME1 Suppressor. Int J Mol Sci 2021; 22:ijms222212194. [PMID: 34830075 PMCID: PMC8619003 DOI: 10.3390/ijms222212194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/02/2021] [Accepted: 11/08/2021] [Indexed: 12/31/2022] Open
Abstract
This study aimed to investigate the effects of the human macrophage (MP) secretome in cellular xenograft rejection. The role of human nucleoside diphosphate kinase A (hNME1), from the secretome of MPs involved in the neuronal differentiation of miniature pig adipose tissue-derived mesenchymal stem cells (mp AD-MSCs), was evaluated by proteomic analysis. Herein, we first demonstrate that hNME1 strongly binds to porcine ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1 (pST8SIA1), which is a ganglioside GD3 synthase. When hNME1 binds with pST8SIA1, it induces degradation of pST8SIA1 in mp AD-MSCs, thereby inhibiting the expression of ganglioside GD3 followed by decreased neuronal differentiation of mp AD-MSCs. Therefore, we produced nanobodies (NBs) named NB-hNME1 that bind to hNME1 specifically, and the inhibitory effect of NB-hNME1 was evaluated for blocking the binding between hNME1 and pST8SIA1. Consequently, NB-hNME1 effectively blocked the binding of hNME1 to pST8SIA1, thereby recovering the expression of ganglioside GD3 and neuronal differentiation of mp AD-MSCs. Our findings suggest that mp AD-MSCs could be a potential candidate for use as an additive, such as an immunosuppressant, in stem cell transplantation.
Collapse
Affiliation(s)
- Jin Hyoung Cho
- Department of Biological Science, College of Natural Sciences, Wonkwang University, 460, Iksan-daero, Iksan-si 54538, Korea; (J.H.C.); (W.S.J.); (S.Y.S.); (J.-G.K.); (S.J.P.)
- GreenBio Corp. Central Research, 201-19, Bubaljungand-ro, Bubal-eup, Icheon-si 17321, Korea
| | - Won Seok Ju
- Department of Biological Science, College of Natural Sciences, Wonkwang University, 460, Iksan-daero, Iksan-si 54538, Korea; (J.H.C.); (W.S.J.); (S.Y.S.); (J.-G.K.); (S.J.P.)
- Institute for Glycoscience, Wonkwang University, 460, Iksan-daero, Iksan-si 54538, Korea
| | - Sang Young Seo
- Department of Biological Science, College of Natural Sciences, Wonkwang University, 460, Iksan-daero, Iksan-si 54538, Korea; (J.H.C.); (W.S.J.); (S.Y.S.); (J.-G.K.); (S.J.P.)
| | - Bo Hyun Kim
- CHA Fertility Center Bundang, 59, Yatap-ro, Bundang-gu, Seongnam-si 13496, Korea;
| | - Ji-Su Kim
- Primate Resources Center (PRC), Korea Research Institute of Bioscience and Biotechnology, 181, Ipsin-gil, Jeongeup-si 56216, Korea;
| | - Jong-Geol Kim
- Department of Biological Science, College of Natural Sciences, Wonkwang University, 460, Iksan-daero, Iksan-si 54538, Korea; (J.H.C.); (W.S.J.); (S.Y.S.); (J.-G.K.); (S.J.P.)
| | - Soon Ju Park
- Department of Biological Science, College of Natural Sciences, Wonkwang University, 460, Iksan-daero, Iksan-si 54538, Korea; (J.H.C.); (W.S.J.); (S.Y.S.); (J.-G.K.); (S.J.P.)
| | - Young-Kug Choo
- Department of Biological Science, College of Natural Sciences, Wonkwang University, 460, Iksan-daero, Iksan-si 54538, Korea; (J.H.C.); (W.S.J.); (S.Y.S.); (J.-G.K.); (S.J.P.)
- Institute for Glycoscience, Wonkwang University, 460, Iksan-daero, Iksan-si 54538, Korea
- Correspondence: ; Tel.: +82-63-850-6087; Fax: +82-63-857-8837
| |
Collapse
|
20
|
Mao Y, Zheng J, Feng S, Tian R. [Comparison of the performance of secretome analysis based on metabolic labeling by three unnatural sugars]. Se Pu 2021; 39:1086-1093. [PMID: 34505430 PMCID: PMC9404127 DOI: 10.3724/sp.j.1123.2021.04017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
分泌蛋白质是调控细胞间信号转导的重要生物大分子。由于分泌蛋白的丰度相比于胞内蛋白以及培养基添加剂更低,因此分泌蛋白的高通量鉴定是目前蛋白质组学界研究的热点和难点。目前,基于生物质谱的分泌蛋白质组学分析一般均需要从无血清的条件培养基中获得分泌蛋白质,再对其进行富集和分析。该流程操作步骤繁琐,易造成分泌蛋白质的损失和降解。本工作采用基于生物正交化学生物学技术实现对分泌蛋白质的高选择性标记和高效富集。通过结合点击化学技术,综合评估了分泌蛋白质分析中用于代谢标记的不同糖类似物。采用3种最常用的商品化糖类似物,N-叠氮乙酰甘露糖胺(ManNAz)、N-叠氮乙酰半乳糖胺(GalNAz)和N-叠氮乙酰葡萄糖胺(GlcNAz)分别对HeLa细胞进行代谢标记,之后通过炔基生物素探针对条件培养基中的分泌蛋白进行富集,结合质谱分析来对比3种糖类似物对分泌蛋白的标记效率。最后通过无标定量蛋白质组学分析,系统评估了3种糖类似物用于分泌蛋白质组分析的性能。结果表明,基于ManNAz的分泌蛋白标记方法鉴定到了282个分泌蛋白、224个细胞质膜蛋白以及846个N-糖基化位点;对分泌蛋白的富集效率分别较GalNAz和GlcNAz提高了130%和67.2%;对细胞质膜蛋白的富集效率较GalNAz和GlcNAz分别提高了273.3%和148.7%,体现出了明显的优势。本研究的实验结果为分泌蛋白高选择性富集和系统分析提供了有益的对比分析和新技术策略。
Collapse
Affiliation(s)
- Yuan Mao
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Jiangnan Zheng
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shun Feng
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Ruijun Tian
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| |
Collapse
|
21
|
Multi-layered proteogenomic analysis unravels cancer metastasis directed by MMP-2 and focal adhesion kinase signaling. Sci Rep 2021; 11:17130. [PMID: 34429501 PMCID: PMC8385024 DOI: 10.1038/s41598-021-96635-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/10/2021] [Indexed: 12/27/2022] Open
Abstract
The role of matrix metalloproteinase-2 (MMP-2) in tumor cell migration has been widely studied, however, the characteristics and effects of MMP-2 in clinical sample of metastatic colorectal cancer (CRC) remain poorly understood. Here, in order to unveil the perturbed proteomic signal during MMP-2 induced cancer progression, we analyzed plasma proteome of CRC patients according to disease progression, HCT116 cancer secretome upon MMP-2 knockdown, and publicly available CRC tissue proteome data. Collectively, the integrative analysis of multi-layered proteomes revealed that a protein cluster containing EMT (Epithelial-to-Mesenchymal Transition)-associated proteins such as CD9-integrin as well as MMP-2. The proteins of the cluster were regulated by MMP-2 perturbation and exhibited significantly increased expressions in tissue and plasma as disease progressed from TNM (Tumor, Node, and Metastasis) stage I to II. Furthermore, we also identified a plausible association between MMP-2 up-regulation and activation of focal adhesion kinase signaling in the proteogenomic analysis of CRC patient tissues. Based on these comparative and integrative analyses, we suggest that the high invasiveness in the metastatic CRC resulted from increased secretion of MMP-2 and CD9-integrin complex mediated by FAK signaling activation.
Collapse
|
22
|
Jaulin N, Idrus RH, Saim A, Wan-Ibrahim WI, Abdul-Rahman PS, Lokanathan Y. Airway Fibroblast Secretory Products Enhance Cell Migration. CURR PROTEOMICS 2021. [DOI: 10.2174/1570164618666210823094105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The nasal fibroblast secretome, which includes various cytokines, chemokines, and growth factors, promotes cell migration. Currently, the proteomics of airway fibroblast (AF) conditioned medium (AFCM) are being actively studied.
Objective:
This study was aimed at profiling and identifying the AF secreted proteins that can enhance wound healing of the airway epithelium and predict the potential pathway involved.
Methods:
Airway epithelial cells (AECs) and AFs were isolated from redundant human nasal turbinate and cultured. AFCM was collected by culturing the AFs either with serum-free airway epithelium basal medium (AECM) or with serum-free F12:DMEM (FDCM). For evaluating cell migration, the AECs were supplemented with airway epithelium medium and defined keratinocyte medium (1:1; AEDK; control), or with AEDK supplemented with 20% AECM or 20% FDCM. The mass spectrometry sample was prepared by protein precipitation, followed by gel electrophoresis and in-gel digestion.
Results :
AECM promoted better cell migration compared to the FDCM and the control medium. Bioinformatics analysis identified a total of 121, and 92 proteins from AECM and FDCM, respectively: 109 and 82 were identified as secreted proteins, respectively. STRING® analysis predicted that 23 proteins from the AECM and 16 proteins from the FDCM are involved in wound healing.
Conclusion:
Conditioned medium promotes wound healing by enhancing cell migration, and we successfully identified various secretory proteins in a conditioned medium that play important roles in wound healing.
Collapse
Affiliation(s)
- Nundisa Jaulin
- Centre for Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Ruszymah Hj Idrus
- Centre for Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Aminuddin Saim
- Ear, Nose and Throat Consultant Clinic, KPJ Ampang Puteri Specialist Hospital, Ampang, Malaysia
| | - Wan Izlina Wan-Ibrahim
- Department of Oral and Craniofacial Sciences, Faculty of Dentistry, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Puteri Shafinaz Abdul-Rahman
- Medical Biotechnology Laboratory, Central Research Laboratories, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Yogeswaran Lokanathan
- Centre for Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| |
Collapse
|
23
|
Liu X, Zhang Y, Ward LD, Yan Q, Bohnuud T, Hernandez R, Lao S, Yuan J, Fan F. A proteomic platform to identify off-target proteins associated with therapeutic modalities that induce protein degradation or gene silencing. Sci Rep 2021; 11:15856. [PMID: 34349202 PMCID: PMC8338952 DOI: 10.1038/s41598-021-95354-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/12/2021] [Indexed: 12/31/2022] Open
Abstract
Novel modalities such as PROTAC and RNAi have the ability to inadvertently alter the abundance of endogenous proteins. Currently available in vitro secondary pharmacology assays, which evaluate off-target binding or activity of small molecules, do not fully assess the off-target effects of PROTAC and are not applicable to RNAi. To address this gap, we developed a proteomics-based platform to comprehensively evaluate the abundance of off-target proteins. First, we selected off-target proteins using genetics and pharmacology evidence. This process yielded 2813 proteins, which we refer to as the “selected off-target proteome” (SOTP). An iterative algorithm was then used to identify four human cell lines out of 932. The 4 cell lines collectively expressed ~ 80% of the SOTP based on transcriptome data. Second, we used mass spectrometry to quantify the intracellular and extracellular proteins from the selected cell lines. Among over 10,000 quantifiable proteins identified, 1828 were part of the predefined SOTP. The SOTP was designed to be easily modified or expanded, owing to the rational selection process developed and the label free LC–MS/MS approach chosen. This versatility inherent to our platform is essential to design fit-for-purpose studies that can address the dynamic questions faced in investigative toxicology.
Collapse
Affiliation(s)
- Xin Liu
- Amgen Inc., Translational Safety and Bioanalytical Sciences, 360 Binney St., Cambridge, MA, 02142, USA.,Novartis Institutes for Biomedical Research, 500 Technology Square, Cambridge, MA, 02139, USA
| | - Ye Zhang
- Amgen Inc., Translational Safety and Bioanalytical Sciences, 360 Binney St., Cambridge, MA, 02142, USA.,Novartis Institutes for Biomedical Research, 500 Technology Square, Cambridge, MA, 02139, USA
| | - Lucas D Ward
- Amgen Inc., Translational Safety and Bioanalytical Sciences, 360 Binney St., Cambridge, MA, 02142, USA.,Alnylam Pharmaceuticals, 300 Third St., Cambridge, MA, 02142, USA
| | - Qinghong Yan
- Amgen Inc., Translational Safety and Bioanalytical Sciences, 360 Binney St., Cambridge, MA, 02142, USA.,Fosun Pharma, 104 Carnegie Center Drive, Suite 204, Princeton, NJ, 08540, USA
| | - Tanggis Bohnuud
- Amgen Inc., Translational Safety and Bioanalytical Sciences, 360 Binney St., Cambridge, MA, 02142, USA.,Beam Pharmaceuticals, 26 Landsdowne St., Cambridge, MA, 02139, USA
| | - Rocio Hernandez
- Amgen Inc., Translational Safety and Bioanalytical Sciences, 360 Binney St., Cambridge, MA, 02142, USA.,Amgen Inc., Translational Safety and Bioanalytical Sciences, 1 Amgen Center Dr., Thousand Oaks, CA, 91320, USA
| | - Socheata Lao
- Amgen Inc., Translational Safety and Bioanalytical Sciences, 360 Binney St., Cambridge, MA, 02142, USA.,Amgen Inc., Translational Safety and Bioanalytical Sciences, 1120 Veteran Blvd, South San Francisco, CA, 94080, USA
| | - Jing Yuan
- Amgen Inc., Translational Safety and Bioanalytical Sciences, 360 Binney St., Cambridge, MA, 02142, USA.,Drug Safety Research and Development, Pfizer Inc., 1 Portland St., Cambridge, MA, 02139, USA
| | - Fan Fan
- Amgen Inc., Translational Safety and Bioanalytical Sciences, 360 Binney St., Cambridge, MA, 02142, USA. .,Amgen Inc., Translational Safety and Bioanalytical Sciences, 1120 Veteran Blvd, South San Francisco, CA, 94080, USA.
| |
Collapse
|
24
|
An YH, Kim DH, Lee EJ, Lee D, Park MJ, Ko J, Kim DW, Koh J, Hong HS, Son Y, Cho JY, Park JU, Kim SD, Hwang NS. High-Efficient Production of Adipose-Derived Stem Cell (ADSC) Secretome Through Maturation Process and Its Non-scarring Wound Healing Applications. Front Bioeng Biotechnol 2021; 9:681501. [PMID: 34222219 PMCID: PMC8242583 DOI: 10.3389/fbioe.2021.681501] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/04/2021] [Indexed: 11/13/2022] Open
Abstract
Recently, the stem cell-derived secretome, which is the set of proteins expressed by stem cells and secreted into the extracellular space, has been demonstrated as a critical contributor for tissue repair. In this study, we have produced two sets of high concentration secretomes from adipose-derived mesenchymal stem cells (ADSCs) that contain bovine serum or free of exogenous molecules. Through proteomic analysis, we elucidated that proteins related to extracellular matrix organization and growth factor-related proteins are highly secreted by ADSCs. Additionally, the application of ADSC secretome to full skin defect showed accelerated wound closure, enhanced angiogenic response, and complete regeneration of epithelial gaps. Furthermore, the ADSC secretome was capable of reducing scar formation. Finally, we show high-dose injection of ADSC secretome via intraperitoneal or transdermal delivery demonstrated no detectable pathological conditions in various tissues/organs, which supports the notion that ADSC secretome can be safely utilized for tissue repair and regeneration.
Collapse
Affiliation(s)
- Young-Hyeon An
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul, South Korea.,BioMax/N-Bio Institute, Seoul National University, Seoul, South Korea
| | | | | | - Dabin Lee
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Mihn Jeong Park
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea
| | - Junghyeon Ko
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul, South Korea
| | - Dong Wook Kim
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Jiwan Koh
- Senior Science & Life, Inc., Seoul, South Korea
| | - Hyun Sook Hong
- Department of Biomedical Science and Technology, Kyung Hee University, Seoul, South Korea
| | - Youngsook Son
- Department of Biomedical Science and Technology, Kyung Hee University, Seoul, South Korea.,Department of Genetic Biotechnology and Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Je-Yoel Cho
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Ji-Ung Park
- Department of Plastic and Reconstructive Surgery, Seoul National University Boramae Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | | | - Nathaniel S Hwang
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul, South Korea.,BioMax/N-Bio Institute, Seoul National University, Seoul, South Korea.,Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea
| |
Collapse
|
25
|
Zheng J, Mao Y, Feng S, Tian R. Combining Metabolic Alkyne Labeling and Click Chemistry for Secretome Analysis of
Serum‐Containing
Conditioned Medium
†. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202000752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jiangnan Zheng
- Department of Chemistry, School of Science, Southern University of Science and Technology Shenzhen Guangdong 518055 China
| | - Yuan Mao
- School of Life Science and Engineering, Southwest Jiaotong University Chengdu Sichuan 610031 China
| | - Shun Feng
- School of Life Science and Engineering, Southwest Jiaotong University Chengdu Sichuan 610031 China
| | - Ruijun Tian
- Department of Chemistry, School of Science, Southern University of Science and Technology Shenzhen Guangdong 518055 China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology 1088 Xueyuan Road Shenzhen Guangdong 518055 China
| |
Collapse
|
26
|
Yao J, Huang X, Ren J. In situ determination of secretory kinase Fam20C from living cells using fluorescence correlation spectroscopy. Talanta 2021; 232:122473. [PMID: 34074441 DOI: 10.1016/j.talanta.2021.122473] [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: 01/31/2021] [Revised: 04/15/2021] [Accepted: 04/23/2021] [Indexed: 11/19/2022]
Abstract
Secretory proteins constitute a biologically crucial subset of proteins for regulation of some pathological and physiological processes, and they have become very important biomarkers in clinical diagnosis and therapeutic targets. So far, secretory protein functions and mechanisms have not been fully understood due to methodological limitations in detection of low-abundance proteins against medium background. Here, we propose a strategy to determine secretory protein from living cells in situ using fluorescence correlation spectroscopy (FCS). In this study, the recombinant protein Fam20C with SNAP-tag was used as a model protein, and O6-benzylguanine (BG) derivatives bearing fluorescent dye as probes. We synthesized three fluorescent probes and investigated their fluorescent properties and diffusion behaviors in solution, and found the probe BG-Bodipy-561 more suitable for in situ labeling of Fam20C. We confirmed the specific binding of the probe to the target protein by combining FCS and in-gel fluorescence scanning methods. We studied the effects of some factors of the secretory Fam20C, and found that RNA interference significantly inhibited the synthesis of secretory fused Fam20C, and myriocin had no significant effect on the expression of secretory Fam20C, which indirectly illustrated that sphingolipid signaling can regulate the Fam20C activity. We believe that FCS is a very promising method to analyze secretory proteins from living cells in situ.
Collapse
Affiliation(s)
- Jun Yao
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
| | - Xiangyi Huang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
| | - Jicun Ren
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
| |
Collapse
|
27
|
Suttapitugsakul S, Tong M, Sun F, Wu R. Enhancing Comprehensive Analysis of Secreted Glycoproteins from Cultured Cells without Serum Starvation. Anal Chem 2021; 93:2694-2705. [PMID: 33397101 PMCID: PMC8034805 DOI: 10.1021/acs.analchem.0c05126] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Glycoproteins secreted by cells play essential roles in the regulation of extracellular activities. Secreted glycoproteins are often reflective of cellular status, and thus glycoproteins from easily accessible bodily fluids can serve as excellent biomarkers for disease detection. Cultured cells have been extensively employed as models in the research fields of biology and biomedicine, and global analysis of glycoproteins secreted from these cells provides insights into cellular activities and glycoprotein functions. However, comprehensive identification and quantification of secreted glycoproteins is a daunting task because of their low abundances compared with the high-abundance serum proteins required for cell growth and proliferation. Several studies employed serum-free media to analyze secreted proteins, but it has been shown that serum starvation, even for a short period of time, can alter protein secretion. To overcome these issues, we developed a method to globally characterize secreted glycoproteins and their N-glycosylation sites from cultured cells by combining selective enrichment of secreted glycoproteins with a boosting approach. The results demonstrated the importance of the boosting sample selection and the boosting-to-sample ratio for improving the coverage of secreted glycoproteins. The method was applied to globally quantify secreted glycoproteins from THP-1 monocytes and macrophages in response to lipopolysaccharides (LPS) and from Hep G2 cells treated with TGF-β without serum starvation. We found differentially secreted glycoproteins in these model systems that showed the cellular response to the immune activation or the epithelial-to-mesenchymal transition. Benefiting from the selective enrichment and the signal enhancement of low-abundance secreted glycoproteins, this method can be extensively applied to study secreted glycoproteins without serum starvation, which will provide a better understanding of protein secretion and cellular activity.
Collapse
Affiliation(s)
- Suttipong Suttapitugsakul
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ming Tong
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Fangxu Sun
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| |
Collapse
|
28
|
Wei W, Riley NM, Yang AC, Kim JT, Terrell SM, Li VL, Garcia-Contreras M, Bertozzi CR, Long JZ. Cell type-selective secretome profiling in vivo. Nat Chem Biol 2020; 17:326-334. [PMID: 33199915 PMCID: PMC7904581 DOI: 10.1038/s41589-020-00698-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/20/2020] [Indexed: 01/06/2023]
Abstract
Secreted polypeptides are a fundamental biochemical axis of intercellular and endocrine communication. However, a global understanding of composition and dynamics of cellular secretomes in intact mammalian organisms has been lacking. Here, we introduce a proximity biotinylation strategy that enables labeling, detection, and enrichment of secreted polypeptides in a cell type-selective manner in mice. We generate a proteomic atlas of hepatocyte, myocyte, pericyte, and myeloid cell secretomes by direct purification of biotinylated secreted proteins from blood plasma. Our secretome dataset validates known cell type-protein pairs, reveals secreted polypeptides that distinguish between cell types, and identifies new cellular sources for classical plasma proteins. Lastly, we uncover a dynamic and previously undescribed nutrient-dependent reprogramming of the hepatocyte secretome characterized by increased unconventional secretion of the cytosolic enzyme BHMT. This secretome profiling strategy enables dynamic and cell-type dissection of the plasma proteome and the secreted polypeptides that mediate intercellular signaling.
Collapse
Affiliation(s)
- Wei Wei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Biology, Stanford University, Stanford, CA, USA.,Stanford ChEM-H, Stanford University, Stanford, CA, USA
| | - Nicholas M Riley
- Stanford ChEM-H, Stanford University, Stanford, CA, USA.,Department of Chemistry, Stanford University, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Andrew C Yang
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Joon T Kim
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Stanford ChEM-H, Stanford University, Stanford, CA, USA
| | - Stephanie M Terrell
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Stanford ChEM-H, Stanford University, Stanford, CA, USA
| | - Veronica L Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Stanford ChEM-H, Stanford University, Stanford, CA, USA.,Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Marta Garcia-Contreras
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Stanford ChEM-H, Stanford University, Stanford, CA, USA
| | - Carolyn R Bertozzi
- Stanford ChEM-H, Stanford University, Stanford, CA, USA.,Department of Chemistry, Stanford University, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Jonathan Z Long
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA. .,Stanford ChEM-H, Stanford University, Stanford, CA, USA.
| |
Collapse
|
29
|
Sukumaran A, Woroszchuk E, Ross T, Geddes-McAlister J. Proteomics of host-bacterial interactions: new insights from dual perspectives. Can J Microbiol 2020; 67:213-225. [PMID: 33027598 DOI: 10.1139/cjm-2020-0324] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mass-spectrometry (MS)-based proteomics is a powerful and robust platform for studying the interactions between biological systems during health and disease. Bacterial infections represent a significant threat to global health and drive the pursuit of novel therapeutic strategies to combat emerging and resistant pathogens. During infection, the interplay between a host and pathogen determines the ability of the microbe to survive in a hostile environment and promotes an immune response by the host as a protective measure. It is the protein-level changes from either biological system that define the outcome of infection, and MS-based proteomics provides a rapid and effective platform to identify such changes. In particular, proteomics detects alterations in protein abundance, quantifies protein secretion and (or) release, measures an array of post-translational modifications that influence signaling cascades, and profiles protein-protein interactions through protein complex and (or) network formation. Such information provides new insight into the role of known and novel bacterial effectors, as well as the outcome of host cell activation. In this Review, we highlight the diverse applications of MS-based proteomics in profiling the relationship between bacterial pathogens and the host. Our work identifies a plethora of strategies for exploring mechanisms of infection from dual perspectives (i.e., host and pathogen), and we suggest opportunities to extrapolate the current knowledgebase to other biological systems for applications in therapeutic discovery.
Collapse
Affiliation(s)
- Arjun Sukumaran
- Molecular and Cellular Biology Department, University of Guelph, Guelph, ON N1G 2W1, Canada.,Molecular and Cellular Biology Department, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Elizabeth Woroszchuk
- Molecular and Cellular Biology Department, University of Guelph, Guelph, ON N1G 2W1, Canada.,Molecular and Cellular Biology Department, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Taylor Ross
- Molecular and Cellular Biology Department, University of Guelph, Guelph, ON N1G 2W1, Canada.,Molecular and Cellular Biology Department, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Jennifer Geddes-McAlister
- Molecular and Cellular Biology Department, University of Guelph, Guelph, ON N1G 2W1, Canada.,Molecular and Cellular Biology Department, University of Guelph, Guelph, ON N1G 2W1, Canada
| |
Collapse
|
30
|
Kleinpenning F, Steigenberger B, Wu W, Heck AJR. Fishing for newly synthesized proteins with phosphonate-handles. Nat Commun 2020; 11:3244. [PMID: 32591520 PMCID: PMC7320153 DOI: 10.1038/s41467-020-17010-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/03/2020] [Indexed: 02/07/2023] Open
Abstract
Bioorthogonal chemistry introduces affinity-labels into biomolecules with minimal disruption to the original system and is widely applicable in a range of contexts. In proteomics, immobilized metal affinity chromatography (IMAC) enables enrichment of phosphopeptides with extreme sensitivity and selectivity. Here, we adapt and combine these superb assets in a new enrichment strategy using phosphonate-handles, which we term PhosID. In this approach, click-able phosphonate-handles are introduced into proteins via 1,3-dipolar Huisgen-cycloaddition to azido-homo-alanine (AHA) and IMAC is then used to enrich exclusively for phosphonate-labeled peptides. In interferon-gamma (IFNγ) stimulated cells, PhosID enabled the identification of a large number of IFN responsive newly synthesized proteins (NSPs) whereby we monitored the differential synthesis of these proteins over time. Collectively, these data validate the excellent performance of PhosID with efficient analysis and quantification of hundreds of NSPs by single LC-MS/MS runs. We envision PhosID as an attractive and alternative tool for studying stimuli-sensitive proteome subsets. Here the authors describe PhosID, an enrichment strategy using phosphonate-handles, that combines click chemistry and IMAC-based phospho-enrichment for quantitative proteomics analysis of newly synthesized proteins.
Collapse
Affiliation(s)
- Fleur Kleinpenning
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Barbara Steigenberger
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands. .,Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands. .,Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| |
Collapse
|
31
|
Oxidative Phosphorylation Dysfunction Modifies the Cell Secretome. Int J Mol Sci 2020; 21:ijms21093374. [PMID: 32397676 PMCID: PMC7246988 DOI: 10.3390/ijms21093374] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/29/2020] [Accepted: 05/09/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondrial oxidative phosphorylation disorders are extremely heterogeneous conditions. Their clinical and genetic variability makes the identification of reliable and specific biomarkers very challenging. Until now, only a few studies have focused on the effect of a defective oxidative phosphorylation functioning on the cell’s secretome, although it could be a promising approach for the identification and pre-selection of potential circulating biomarkers for mitochondrial diseases. Here, we review the insights obtained from secretome studies with regard to oxidative phosphorylation dysfunction, and the biomarkers that appear, so far, to be promising to identify mitochondrial diseases. We propose two new biomarkers to be taken into account in future diagnostic trials.
Collapse
|
32
|
Swietlik JJ, Sinha A, Meissner F. Dissecting intercellular signaling with mass spectrometry-based proteomics. Curr Opin Cell Biol 2020; 63:20-30. [PMID: 31927463 DOI: 10.1016/j.ceb.2019.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/27/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023]
Abstract
Physiological functions depend on a coordinated interplay of numerous different cell types. Proteins serve as major signaling molecules between cells; however, their comprehensive investigation in physiologically relevant settings has remained challenging. Mass spectrometry (MS)-based shotgun proteomics is emerging as a powerful technology for the systematic analysis of protein-mediated intercellular signaling and regulated post-translational modifications. Here, we discuss recent advancements in cell biological, chemical, and biochemical MS-based approaches for the profiling of cellular messengers released by sending cells, receptors expressed on the cell surface, and their interactions. We highlight methods tailored toward the mapping of dynamic signal transduction mechanisms at cellular interfaces and approaches to dissect communication cell specifically in heterocellular systems. Thereby, MS-based proteomics contributes a unique systems biology perspective for the identification of intercellular signaling pathways deregulated in disease.
Collapse
Affiliation(s)
- Jonathan J Swietlik
- Experimental Systems Immunology Laboratory, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Ankit Sinha
- Experimental Systems Immunology Laboratory, Max-Planck Institute of Biochemistry, Martinsried, Germany; Institute of Translational Cancer Research and Experimental Cancer Therapy, Klinikum Rechts der Isar, TU München, Munich, Germany
| | - Felix Meissner
- Experimental Systems Immunology Laboratory, Max-Planck Institute of Biochemistry, Martinsried, Germany.
| |
Collapse
|
33
|
Affiliation(s)
| | | | - Ronghu Wu
- School of Chemistry and Biochemistry and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| |
Collapse
|
34
|
Shin J, Kwon Y, Lee S, Na S, Hong EY, Ju S, Jung HG, Kaushal P, Shin S, Back JH, Choi SY, Kim EH, Lee SJ, Park YE, Ahn HS, Ahn Y, Kabir MH, Park SJ, Yang WS, Yeom J, Bang OY, Ha CW, Lee JW, Kang UB, Kim HJ, Park KS, Lee JE, Lee JE, Kim JY, Kim KP, Kim Y, Hirano H, Yi EC, Cho JY, Paek E, Lee C. Common Repository of FBS Proteins (cRFP) To Be Added to a Search Database for Mass Spectrometric Analysis of Cell Secretome. J Proteome Res 2019; 18:3800-3806. [PMID: 31475827 DOI: 10.1021/acs.jproteome.9b00475] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We propose to use cRFP (common Repository of FBS Proteins) in the MS (mass spectrometry) raw data search of cell secretomes. cRFP is a small supplementary sequence list of highly abundant fetal bovine serum proteins added to the reference database in use. The aim behind using cRFP is to prevent the contaminant FBS proteins from being misidentified as other proteins in the reference database, just as we would use cRAP (common Repository of Adventitious Proteins) to prevent contaminant proteins present either by accident or through unavoidable contacts from being misidentified as other proteins. We expect it to be widely used in experiments where the proteins are obtained from serum-free media after thorough washing of the cells, or from a complex media such as SILAC, or from extracellular vesicles directly.
Collapse
Affiliation(s)
- Jihye Shin
- Center for Theragnosis, Korea Institute of Science and Technology , Seoul 02792 , Korea.,Advanced Medical Research Center , Yokohama City University , Kanazawa , Yokohama 236-0004 , Japan
| | - Yumi Kwon
- Center for Theragnosis, Korea Institute of Science and Technology , Seoul 02792 , Korea.,Department of Life Science and Research Institute for Natural Sciences , Hanyang University , Seoul 04763 , Korea
| | - Seonjeong Lee
- Center for Theragnosis, Korea Institute of Science and Technology , Seoul 02792 , Korea.,Division of Bio-Medical Science & Technology, KIST School , Korea University of Science and Technology , Seoul 02792 , Korea
| | - Seungjin Na
- Department of Computer Science , Hanyang University , Seoul 04763 , Korea
| | - Eun Young Hong
- Center for Theragnosis, Korea Institute of Science and Technology , Seoul 02792 , Korea
| | - Shinyeong Ju
- Center for Theragnosis, Korea Institute of Science and Technology , Seoul 02792 , Korea.,Department of Life Science and Research Institute for Natural Sciences , Hanyang University , Seoul 04763 , Korea
| | - Hyun-Gyo Jung
- Center for Theragnosis, Korea Institute of Science and Technology , Seoul 02792 , Korea.,Division of Bio-Medical Science & Technology, KIST School , Korea University of Science and Technology , Seoul 02792 , Korea
| | - Prashant Kaushal
- Center for Theragnosis, Korea Institute of Science and Technology , Seoul 02792 , Korea.,Division of Bio-Medical Science & Technology, KIST School , Korea University of Science and Technology , Seoul 02792 , Korea
| | - Sungho Shin
- Center for Theragnosis, Korea Institute of Science and Technology , Seoul 02792 , Korea.,KHU-KIST Department of Converging Science and Technology , Kyung Hee University , Seoul 02447 , Korea
| | - Ji Hyun Back
- Center for Theragnosis, Korea Institute of Science and Technology , Seoul 02792 , Korea.,Department of Biotechnology, College of Life Sciences and Biotechnology , Korea University , Seoul 02841 , Korea
| | - Seon Young Choi
- Department of Health Sciences and Technology, SAIHST , Sungkyunkwan University , Seoul 06351 , Korea.,Stem Cell & Regenerative Medicine Institute , Samsung Medical Center , Seoul 06351 , Korea
| | - Eun Hee Kim
- Stem Cell & Regenerative Medicine Institute , Samsung Medical Center , Seoul 06351 , Korea
| | - Su Jin Lee
- Center for Theragnosis, Korea Institute of Science and Technology , Seoul 02792 , Korea.,Department of Life Science, College of Natural Sciences , Ewha Womans University , Seoul 03760 , Korea
| | - Yae Eun Park
- Center for Theragnosis, Korea Institute of Science and Technology , Seoul 02792 , Korea.,Department of Biochemistry, College of Life Science and Biotechnology , Yonsei University , Seoul 03722 , Korea
| | - Hee-Sung Ahn
- Asan Institute for Life Sciences , Asan Medical Center , Seoul 05505 , Korea
| | - Younghee Ahn
- Departments of Pediatrics, Clinical Neurosciences, Physiology & Pharmacology, Alberta Children's Hospital Research Institute, Cumming School of Medicine , University of Calgary , Calgary , Alberta T2N 1N4 , Canada
| | | | | | - Won Suk Yang
- R&D Center for Clinical Mass Spectrometry , Seegene Medical Foundation , Seoul 04805 , Korea
| | - Jeonghun Yeom
- Toxicological Laboratory, Department of Emergency Medicine , Asan Medical Center , Seoul 05505 , Korea
| | - Oh Young Bang
- Departments of Neurology, Samsung Medical Center , Sungkyunkwan University , Seoul 06351 , Korea
| | - Chul-Won Ha
- Department of Health Sciences and Technology, SAIHST , Sungkyunkwan University , Seoul 06351 , Korea.,Stem Cell & Regenerative Medicine Institute , Samsung Medical Center , Seoul 06351 , Korea.,Department of Orthopedic Surgery, Samsung Medical Center , Sungkyunkwan University School of Medicine , Seoul 06351 , Korea
| | - Jin-Won Lee
- Department of Life Science and Research Institute for Natural Sciences , Hanyang University , Seoul 04763 , Korea
| | - Un-Beom Kang
- Core Protein Resources Center , Daegu Gyeongbuk Institute of Science and Technology , Daegu 42988 , Korea
| | - Hye-Jung Kim
- New Drug Development Center , KBIO Osong Medical Innovation Foundation , Cheongju-si , Chungbuk 28160 , Korea
| | - Kang-Sik Park
- KHU-KIST Department of Converging Science and Technology , Kyung Hee University , Seoul 02447 , Korea.,Department of Physiology, School of Medicine , Kyung Hee Univeristy , Seoul 02447 , Korea
| | - J Eugene Lee
- Center for Bioanalysis , Korea Research Institute of Standards and Science , Daejeon 34113 , Korea
| | - Ji Eun Lee
- Center for Theragnosis, Korea Institute of Science and Technology , Seoul 02792 , Korea
| | - Jin Young Kim
- Biomedical Omics Research Group , Korea Basic Research Institute , Ochang , Chungbuk 28119 , Korea
| | - Kwang Pyo Kim
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials , Kyung Hee University , Yongin , Gyeonggi 17104 , Korea.,Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute , Kyung Hee University , Seoul 02453 , Korea
| | - Youngsoo Kim
- Department of Biomedical Engineering , Seoul National University College of Medicine , Seoul 03080 , Korea
| | - Hisashi Hirano
- Advanced Medical Research Center , Yokohama City University , Kanazawa , Yokohama 236-0004 , Japan
| | - Eugene C Yi
- Department of Molecular Medicine and Biopharmaceutical Sciences , Seoul National University , Seoul 03080 , Korea
| | - Je-Yoel Cho
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine , Seoul National University , Seoul 08826 , Korea
| | - Eunok Paek
- Department of Computer Science , Hanyang University , Seoul 04763 , Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology , Seoul 02792 , Korea.,Division of Bio-Medical Science & Technology, KIST School , Korea University of Science and Technology , Seoul 02792 , Korea.,KHU-KIST Department of Converging Science and Technology , Kyung Hee University , Seoul 02447 , Korea
| |
Collapse
|
35
|
Song P, Kwon Y, Joo JY, Kim DG, Yoon JH. Secretomics to Discover Regulators in Diseases. Int J Mol Sci 2019; 20:ijms20163893. [PMID: 31405033 PMCID: PMC6720857 DOI: 10.3390/ijms20163893] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/01/2019] [Accepted: 08/08/2019] [Indexed: 01/03/2023] Open
Abstract
Secretory proteins play important roles in the cross-talk of individual functional units, including cells. Since secretory proteins are essential for signal transduction, they are closely related with disease development, including metabolic and neural diseases. In metabolic diseases, adipokines, myokines, and hepatokines are secreted from respective organs under specific environmental conditions, and play roles in glucose homeostasis, angiogenesis, and inflammation. In neural diseases, astrocytes and microglia cells secrete cytokines and chemokines that play roles in neurotoxic and neuroprotective responses. Mass spectrometry-based secretome profiling is a powerful strategy to identify and characterize secretory proteins. This strategy involves stepwise processes such as the collection of conditioned medium (CM) containing secretome proteins and concentration of the CM, peptide preparation, mass analysis, database search, and filtering of secretory proteins; each step requires certain conditions to obtain reliable results. Proteomic analysis of extracellular vesicles has become a new research focus for understanding the additional extracellular functions of intracellular proteins. Here, we provide a review of the insights obtained from secretome analyses with regard to disease mechanisms, and highlight the future prospects of this technology. Continued research in this field is expected to provide valuable information on cell-to-cell communication and uncover new pathological mechanisms.
Collapse
Affiliation(s)
- Parkyong Song
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan 50612, Korea
| | - Yonghoon Kwon
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Jae-Yeol Joo
- Neurodegenerative Disease Research Group, Korea Brain Research Institute, Daegu 41062, Korea
| | - Do-Geun Kim
- Dementia Research Group, Korea Brain Research Institute, Daegu 41062, Korea
| | - Jong Hyuk Yoon
- Neurodegenerative Disease Research Group, Korea Brain Research Institute, Daegu 41062, Korea.
| |
Collapse
|