1
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Gianazza E, Brioschi M, Eligini S, Banfi C. Mass spectrometry for the study of adipocyte cell secretome in cardiovascular diseases. MASS SPECTROMETRY REVIEWS 2024; 43:752-781. [PMID: 36161723 DOI: 10.1002/mas.21812] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/04/2022] [Accepted: 09/03/2022] [Indexed: 06/16/2023]
Abstract
Adipose tissue is classically considered the primary site of lipid storage, but in recent years has garnered appreciation for its broad role as an endocrine organ, capable of remotely signaling to other tissues to alter their metabolic program. The adipose tissue is now recognized as a crucial regulator of cardiovascular health, mediated by the secretion of several bioactive products, with a wide range of endocrine and paracrine effects on the cardiovascular system. Thanks to the development and improvement of high-throughput mass spectrometry, the size and components of the human secretome have been characterized. In this review, we summarized the recent advances in mass spectrometry-based studies of the cell and tissue secretome for the understanding of adipose tissue biology, which may help to decipher the complex molecular mechanisms controlling the crosstalk between the adipose tissue and the cardiovascular system, and their possible clinical translation.
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Affiliation(s)
- Erica Gianazza
- Centro Cardiologico Monzino IRCCS, Unit of Functional Proteomics, Metabolomics and Network Analysis, Milan, Italy
| | - Maura Brioschi
- Centro Cardiologico Monzino IRCCS, Unit of Functional Proteomics, Metabolomics and Network Analysis, Milan, Italy
| | - Sonia Eligini
- Centro Cardiologico Monzino IRCCS, Unit of Functional Proteomics, Metabolomics and Network Analysis, Milan, Italy
| | - Cristina Banfi
- Centro Cardiologico Monzino IRCCS, Unit of Functional Proteomics, Metabolomics and Network Analysis, Milan, Italy
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2
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Noor Azlan NAB, Vitus V, Nor Rashid N, Nordin F, Tye GJ, Wan Kamarul Zaman WS. Human mesenchymal stem cell secretomes: Factors affecting profiling and challenges in clinical application. Cell Tissue Res 2024; 395:227-250. [PMID: 38244032 DOI: 10.1007/s00441-023-03857-4] [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: 06/02/2023] [Accepted: 12/21/2023] [Indexed: 01/22/2024]
Abstract
The promising field of regenerative medicine is thrilling as it can repair and restore organs for various debilitating diseases. Mesenchymal stem cells are one of the main components in regenerative medicine that work through the release of secretomes. By adopting the use of the secretome in cell-free-based therapy, we may be able to address the challenges faced in cell-based therapy. As one of the components of cell-free-based therapy, secretome has the advantage of a better safety and efficacy profile than mesenchymal stem cells. However, secretome has its challenges that need to be addressed, such as its bioprocessing methods that may impact the secretome content and its mechanisms of action in clinical settings. Effective and standardization of bioprocessing protocols are important to ensure the supply and sustainability of secretomes for clinical applications. This may eventually impact its commercialization and marketability. In this review, the bioprocessing methods and their impacts on the secretome profile and treatment are discussed. This improves understanding of its fundamental aspects leading to potential clinical applications.
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Affiliation(s)
| | - Vieralynda Vitus
- Department of Biomedical Engineering, Faculty of Engineering, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
- Centre for Innovation in Medical Engineering, Department of Biomedical Engineering, Faculty of Engineering, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Nurshamimi Nor Rashid
- Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Fazlina Nordin
- Centre for Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Gee Jun Tye
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Minden, Pulau Pinang, Malaysia
| | - Wan Safwani Wan Kamarul Zaman
- Department of Biomedical Engineering, Faculty of Engineering, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
- Centre for Innovation in Medical Engineering, Department of Biomedical Engineering, Faculty of Engineering, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
- Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
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3
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Abstract
Tumor immunology is undergoing a renaissance due to the recent profound clinical successes of tumor immunotherapy. These advances have coincided with an exponential growth in the development of -omics technologies. Armed with these technologies and their associated computational and modeling toolsets, systems biologists have turned their attention to tumor immunology in an effort to understand the precise nature and consequences of interactions between tumors and the immune system. Such interactions are inherently multivariate, spanning multiple time and size scales, cell types, and organ systems, rendering systems biology approaches particularly amenable to their interrogation. While in its infancy, the field of 'Cancer Systems Immunology' has already influenced our understanding of tumor immunology and immunotherapy. As the field matures, studies will move beyond descriptive characterizations toward functional investigations of the emergent behavior that govern tumor-immune responses. Thus, Cancer Systems Immunology holds incredible promise to advance our ability to fight this disease.
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Affiliation(s)
| | - Edgar G Engleman
- Department of Pathology, Stanford University School of MedicineStanfordUnited States
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of MedicineStanfordUnited States
- Stanford Cancer Institute, Stanford UniversityStanfordUnited States
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4
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Dang X, Coimbra R, Mao L, Podvin S, Li X, Yu H, Costantini TW, Zeng X, Larocca D, Eliceiri BP, Baird A. Open reading frame mining identifies a TLR4 binding domain in the primary sequence of ECRG4. Cell Mol Life Sci 2019; 76:5027-5039. [PMID: 31190084 PMCID: PMC11105628 DOI: 10.1007/s00018-019-03159-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/29/2019] [Accepted: 05/22/2019] [Indexed: 01/22/2023]
Abstract
The embedding of small peptide ligands within large inactive pre-pro-precursor proteins encoded by orphan open reading frames (ORFs) makes them difficult to identify and study. To address this problem, we generated oligonucleotide (< 100-400 base pair) combinatorial libraries from either the epidermal growth factor (EGF) ORF that encodes the > 1200 amino acid EGF precursor protein or the orphan ECRG4 ORF, that encodes a 148 amino acid Esophageal Cancer Related Gene 4 (ECRG4), a putative cytokine precursor protein of up to eight ligands. After phage display and 3-4 rounds of biopanning for phage internalization into prostate cancer epithelial cells, sequencing identified the 53-amino acid EGF ligand encoded by the 5' region of the EGF ORF and three distinct domains within the primary sequence of ECRG4: its membrane targeting hydrophobic signal peptide, an unanticipated amino terminus domain at ECRG437-63 and a C-terminus ECRG4133-148 domain. Using HEK-blue cells transfected with the innate immunity receptor complex, we show that both ECRG437-63 and ECRG4133-148 enter cells by interaction with the TLR4 immune complex but neither stimulate NFkB. Taken together, the results help establish that phage display can be used to identify cryptic domains within ORFs of the human secretome and identify a novel TLR4-targeted internalization domain in the amino terminus of ECRG4 that may contribute to its effects on cell migration, immune cell activation and tumor suppression.
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Affiliation(s)
- Xitong Dang
- Department of Surgery, University of California San Diego, San Diego, CA, 92103, USA
- The Key Laboratory of Medical Electrophysiology, Ministry of Education, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, 646000, China
| | - Raul Coimbra
- Department of Surgery, University of California San Diego, San Diego, CA, 92103, USA
| | - Liang Mao
- The Key Laboratory of Medical Electrophysiology, Ministry of Education, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, 646000, China
| | - Sonia Podvin
- Department of Surgery, University of California San Diego, San Diego, CA, 92103, USA
| | - Xue Li
- The Key Laboratory of Medical Electrophysiology, Ministry of Education, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, 646000, China
| | - Hua Yu
- The Key Laboratory of Medical Electrophysiology, Ministry of Education, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, 646000, China
| | - Todd W Costantini
- Department of Surgery, University of California San Diego, San Diego, CA, 92103, USA
| | - Xiaorong Zeng
- The Key Laboratory of Medical Electrophysiology, Ministry of Education, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, 646000, China
| | | | - Brian P Eliceiri
- Department of Surgery, University of California San Diego, San Diego, CA, 92103, USA
| | - Andrew Baird
- Department of Surgery, University of California San Diego, San Diego, CA, 92103, USA.
- Department of Surgery, University of California San Diego, La Jolla, San Diego, CA, 98896, USA.
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5
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Dowling P, Murphy S, Zweyer M, Raucamp M, Swandulla D, Ohlendieck K. Emerging proteomic biomarkers of X-linked muscular dystrophy. Expert Rev Mol Diagn 2019; 19:739-755. [PMID: 31359811 DOI: 10.1080/14737159.2019.1648214] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Progressive skeletal muscle wasting is the manifesting symptom of Duchenne muscular dystrophy, an X-linked inherited disorder triggered by primary abnormalities in the DMD gene. The almost complete loss of dystrophin isoform Dp427 causes a multi-system pathology that features in addition to skeletal muscle weakness also late-onset cardio-respiratory deficiencies, impaired metabolism and abnormalities in the central nervous system. Areas covered: This review focuses on the mass spectrometry-based proteomic characterization of X-linked muscular dystrophy with special emphasis on the identification of novel biomarker candidates in skeletal muscle tissues, as well as non-muscle tissues and various biofluids. Individual sections focus on molecular and cellular aspects of the pathogenic changes in dystrophinopathy, proteomic workflows used in biomarker research, the proteomics of the dystrophin-glycoprotein complex and the potential usefulness of newly identified protein markers involved in fibre degeneration, fibrosis and inflammation. Expert opinion: The systematic application of large-scale proteomic surveys has identified a distinct cohort of both tissue- and biofluid-associated protein species with considerable potential for improving diagnostic, prognostic and therapy-monitoring procedures. Novel proteomic markers include components involved in fibre contraction, cellular signalling, ion homeostasis, cellular stress response, energy metabolism and the immune response, as well as maintenance of the cytoskeletal and extracellular matrix.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland , Kildare , Ireland.,Human Health Research Institute, Maynooth University , Kildare , Ireland
| | - Sandra Murphy
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University , Newcastle upon Tyne , UK
| | - Margit Zweyer
- Institute of Physiology II, University of Bonn , Bonn , Germany
| | - Maren Raucamp
- Institute of Physiology II, University of Bonn , Bonn , Germany
| | | | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland , Kildare , Ireland.,Human Health Research Institute, Maynooth University , Kildare , Ireland
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6
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Pazopanib-induced changes in protein expression signatures of extracellular vesicles in synovial sarcoma. Biochem Biophys Res Commun 2018; 506:723-730. [DOI: 10.1016/j.bbrc.2018.10.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 10/02/2018] [Indexed: 01/14/2023]
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7
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Mustafa S, Pan L, Marzoq A, Fawaz M, Sander L, Rückert F, Schrenk A, Hartl C, Uhler R, Yildirim A, Strobel O, Hackert T, Giese N, Büchler MW, Hoheisel JD, Alhamdani MSS. Comparison of the tumor cell secretome and patient sera for an accurate serum-based diagnosis of pancreatic ductal adenocarcinoma. Oncotarget 2017; 8:11963-11976. [PMID: 28060763 PMCID: PMC5355318 DOI: 10.18632/oncotarget.14449] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 12/25/2016] [Indexed: 01/05/2023] Open
Abstract
Pancreatic cancer is the currently most lethal malignancy. Toward an accurate diagnosis of the disease in body liquids, we studied the protein composition of the secretomes of 16 primary and established cell lines of pancreatic ductal adenocarcinoma (PDAC). Compared to the secretome of non-tumorous cells, 112 proteins exhibited significantly different abundances. Functionally, the proteins were associated with PDAC features, such as decreased apoptosis, better cell survival and immune cell regulation. The result was compared to profiles obtained from 164 serum samples from two independent cohorts - a training and a test set - of patients with PDAC or chronic pancreatitis and healthy donors. Eight of the 112 secretome proteins exhibited similar variations in their abundance in the serum profile specific for PDAC patients, which was composed of altogether 189 proteins. The 8 markers shared by secretome and serum yielded a 95.1% accuracy of distinguishing PDAC from healthy in a Receiver Operating Characteristic curve analysis, while any number of serum-only markers produced substantially less accurate results. Utility of the identified markers was confirmed by classical enzyme linked immunosorbent assays (ELISAs). The study highlights the value of cell secretome analysis as a means of defining reliable serum biomarkers.
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Affiliation(s)
- Shakhawan Mustafa
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany.,Kurdistan Institution for Strategic Studies and Scientific Research, Kurdistan Region, Iraq
| | - Longqiang Pan
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Aseel Marzoq
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Malak Fawaz
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Laureen Sander
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Felix Rückert
- Chirurgische Klinik, Universitätsmedizin Mannheim, Theodor-Kutzer-Ufer 1-3, Mannheim, Germany
| | - Andrea Schrenk
- Chirurgische Klinik, Universitätsmedizin Mannheim, Theodor-Kutzer-Ufer 1-3, Mannheim, Germany
| | - Christina Hartl
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Rico Uhler
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Adem Yildirim
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Oliver Strobel
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Thilo Hackert
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Nathalia Giese
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Markus W Büchler
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
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8
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Kamhieh-Milz J, Mustafa SA, Sterzer V, Celik H, Keski S, Khorramshahi O, Movassaghi K, Hoheisel JD, Alhamdani MSS, Salama A. Secretome profiling of apheresis platelet supernatants during routine storage via antibody-based microarray. J Proteomics 2016; 150:74-85. [PMID: 27478071 DOI: 10.1016/j.jprot.2016.07.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 07/25/2016] [Accepted: 07/27/2016] [Indexed: 02/07/2023]
Abstract
Platelet storage lesions (PSLs) occur during platelet concentrate (PC) storage. Adverse transfusion reactions (ATRs) have been demonstrated to be more frequent in older PCs and removal of the supernatant prior to transfusion reduces their occurrence. Proteomic profiling of PC supernatants was thus performed to identify proteins associated with PSLs and ATRs. Twenty-four PCs were investigated daily from day 0 to day 9 for platelet pre-activation (PPA), platelet-derived extracellular vesicles (PEVs), and platelet function. Using antibody microarrays, 673 extracellular proteins were analysed in PC supernatants on days 0, 3, 5, 7, and 9. During 5days of storage, PPA and PEVs continuously increased (P<0.0001). Platelet function was observed to remain stable within the first 5days (P=0.1751) and decreased thereafter. Comparison of all time points to day 0 revealed the identification of 136 proteins that were significantly changed in abundance during storage, of which 72 were expressed by platelets. Network analysis identified these proteins to be predominantly associated with exosomes (P=4.61×10-8, n=45 genes) and two clusters with distinct functions were found with one being associated with haemostasis and the other with RNA binding. These findings may provide an explanation for ATRs. SIGNIFICANCE Changes in platelet concentrate (PC) supernatants during storage have been so far only poorly addressed and high abundant proteins burden the identification of quantitative changes in the secretome. We applied a high-throughput antibody microarray allowing for the sensitive quantification of 673 extracellular factors. PCs account for the highest number of adverse transfusion reactions (ATRs). ATRs have been demonstrated to be more frequent in older PCs and removal of the supernatant prior to transfusion reduces their occurrence. Comprehensive interpretation of the changing proteins in the secretome during platelet storage under blood banking conditions may help to identify mechanisms leading to the occurrence of adverse transfusion reactions.
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Affiliation(s)
- Julian Kamhieh-Milz
- Institute of Transfusion Medicine, Charité University Medicine Berlin, Augustenburger Platz 1, 13349 Berlin, Germany.
| | - Shakhawan A Mustafa
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Kurdistan Institution for Strategic Studies and Scientific Research, Gullabax 335, Shorsh St., Sulaimani, Kurdistan Region, Iraq
| | - Viktor Sterzer
- Institute of Transfusion Medicine, Charité University Medicine Berlin, Augustenburger Platz 1, 13349 Berlin, Germany
| | - Hatice Celik
- Institute of Transfusion Medicine, Charité University Medicine Berlin, Augustenburger Platz 1, 13349 Berlin, Germany
| | - Sahime Keski
- Institute of Transfusion Medicine, Charité University Medicine Berlin, Augustenburger Platz 1, 13349 Berlin, Germany
| | - Omid Khorramshahi
- Institute of Transfusion Medicine, Charité University Medicine Berlin, Augustenburger Platz 1, 13349 Berlin, Germany
| | - Kamran Movassaghi
- Institute of Transfusion Medicine, Charité University Medicine Berlin, Augustenburger Platz 1, 13349 Berlin, Germany
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Mohamed S S Alhamdani
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Abdulgabar Salama
- Institute of Transfusion Medicine, Charité University Medicine Berlin, Augustenburger Platz 1, 13349 Berlin, Germany
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9
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Lin YL, Huang YJ, Teerapanich P, Leïchlé T, Chou CF. Multiplexed immunosensing and kinetics monitoring in nanofluidic devices with highly enhanced target capture efficiency. BIOMICROFLUIDICS 2016; 10:034114. [PMID: 27375819 PMCID: PMC4902814 DOI: 10.1063/1.4953140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 05/16/2016] [Indexed: 05/21/2023]
Abstract
Nanofluidic devices promise high reaction efficiency and fast kinetic responses due to the spatial constriction of transported biomolecules with confined molecular diffusion. However, parallel detection of multiple biomolecules, particularly proteins, in highly confined space remains challenging. This study integrates extended nanofluidics with embedded protein microarray to achieve multiplexed real-time biosensing and kinetics monitoring. Implementation of embedded standard-sized antibody microarray is attained by epoxy-silane surface modification and a room-temperature low-aspect-ratio bonding technique. An effective sample transport is achieved by electrokinetic pumping via electroosmotic flow. Through the nanoslit-based spatial confinement, the antigen-antibody binding reaction is enhanced with ∼100% efficiency and may be directly observed with fluorescence microscopy without the requirement of intermediate washing steps. The image-based data provide numerous spatially distributed reaction kinetic curves and are collectively modeled using a simple one-dimensional convection-reaction model. This study represents an integrated nanofluidic solution for real-time multiplexed immunosensing and kinetics monitoring, starting from device fabrication, protein immobilization, device bonding, sample transport, to data analysis at Péclet number less than 1.
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10
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Rocha B, Calamia V, Blanco FJ, Ruiz-Romero C. Identification of Factors Produced and Secreted by Mesenchymal Stromal Cells with the SILAC Method. Methods Mol Biol 2016; 1416:551-565. [PMID: 27236695 DOI: 10.1007/978-1-4939-3584-0_33] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Mesenchymal stromal cells (MSCs) secrete a large variety of proteins and factors, which shape the secretome. These proteins participate in multiple cellular functions, including the promotion of regenerative processes in the damaged tissue. Secretomes derived from either undifferentiated MSCs or these cells undergoing osteogenic, chondrogenic, or adipogenic differentiation have been characterized using different liquid chromatography tandem mass spectrometry (LC-MS/MS)-based quantitative proteomic approaches. In this chapter, we describe the use of the Stable Isotope Labeling by Amino Acids in Cell culture (SILAC) strategy for the identification and relative quantification of the mesenchymal stromal cell secretome, specifically during chondrogenesis.
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Affiliation(s)
- Beatriz Rocha
- Rheumatology Division, ProteoRed-PRB2/ISCIII Proteomics Group, INIBIC - Hospital Universitario de A Coruña, A Coruña, 15006, Spain
| | - Valentina Calamia
- Rheumatology Division, ProteoRed-PRB2/ISCIII Proteomics Group, INIBIC - Hospital Universitario de A Coruña, A Coruña, 15006, Spain
| | - Francisco J Blanco
- Rheumatology Division, ProteoRed-PRB2/ISCIII Proteomics Group, INIBIC - Hospital Universitario de A Coruña, A Coruña, 15006, Spain
- RIER-RED de Inflamación y Enfermedades Reumáticas, INIBIC-CHUAC, A Coruña, Spain
- Servicio de Reumatología, Unidad de Investigación, INIBIC-CHU A Coruña, C/Xubias, 84, A Coruña, 15006, Spain
| | - Cristina Ruiz-Romero
- Rheumatology Division, ProteoRed-PRB2/ISCIII Proteomics Group, INIBIC - Hospital Universitario de A Coruña, A Coruña, 15006, Spain.
- CIBER-BBN, INIBIC-CHUAC, A Coruña, Spain.
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11
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Fujita H, Esaki T, Masujima T, Hotta A, Kim SH, Noji H, Watanabe TM. Comprehensive chemical secretory measurement of single cells trapped in a micro-droplet array with mass spectrometry. RSC Adv 2015. [DOI: 10.1039/c4ra12021c] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
By trapping individual single cells in a micro-well, molecules secreted by a single cell can be analyzed using mass spectrometry.
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Affiliation(s)
- Hideaki Fujita
- Immunology Frontier Research Center
- Osaka University
- Suita-shi
- Japan
- Laboratory for Comprehensive Bioimaging
| | - Tsuyoshi Esaki
- Laboratory for single cell mass spectrometry
- Quantitative Biology Center
- RIKEN
- Suita-shi
- Japan
| | - Tsutomu Masujima
- Laboratory for single cell mass spectrometry
- Quantitative Biology Center
- RIKEN
- Suita-shi
- Japan
| | - Akitsu Hotta
- Centar for iPS Cell Research and Application
- Kyoto University
- Sakyo-ku
- Japan
- PRESTO
| | - Soo Hyeon Kim
- Department of Applied Chemistry
- School of Engineering
- The University of Tokyo
- Tokyo 113-8654
- Japan
| | - Hiroyuki Noji
- Department of Applied Chemistry
- School of Engineering
- The University of Tokyo
- Tokyo 113-8654
- Japan
| | - Tomonobu M. Watanabe
- Immunology Frontier Research Center
- Osaka University
- Suita-shi
- Japan
- Laboratory for Comprehensive Bioimaging
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12
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Stenken JA, Poschenrieder AJ. Bioanalytical chemistry of cytokines--a review. Anal Chim Acta 2015; 853:95-115. [PMID: 25467452 PMCID: PMC4717841 DOI: 10.1016/j.aca.2014.10.009] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/30/2014] [Accepted: 10/08/2014] [Indexed: 02/06/2023]
Abstract
Cytokines are bioactive proteins produced by many different cells of the immune system. Due to their role in different inflammatory disease states and maintaining homeostasis, there is enormous clinical interest in the quantitation of cytokines. The typical standard methods for quantitation of cytokines are immunoassay-based techniques including enzyme-linked immusorbent assays (ELISA) and bead-based immunoassays read by either standard or modified flow cytometers. A review of recent developments in analytical methods for measurements of cytokine proteins is provided. This review briefly covers cytokine biology and the analysis challenges associated with measurement of these biomarker proteins for understanding both health and disease. New techniques applied to immunoassay-based assays are presented along with the uses of aptamers, electrochemistry, mass spectrometry, optical resonator-based methods. Methods used for elucidating the release of cytokines from single cells as well as in vivo collection methods are described.
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Affiliation(s)
- Julie A Stenken
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA.
| | - Andreas J Poschenrieder
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA; Pharmaceutical Radiochemistry, Technische Universität München, Walther-Meißner-Street 3, D-85748 Garching, Germany
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13
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Spindel S, Sapsford KE. Evaluation of optical detection platforms for multiplexed detection of proteins and the need for point-of-care biosensors for clinical use. SENSORS (BASEL, SWITZERLAND) 2014; 14:22313-41. [PMID: 25429414 PMCID: PMC4299016 DOI: 10.3390/s141222313] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 11/12/2014] [Accepted: 11/13/2014] [Indexed: 11/16/2022]
Abstract
This review investigates optical sensor platforms for protein multiplexing, the ability to analyze multiple analytes simultaneously. Multiplexing is becoming increasingly important for clinical needs because disease and therapeutic response often involve the interplay between a variety of complex biological networks encompassing multiple, rather than single, proteins. Multiplexing is generally achieved through one of two routes, either through spatial separation on a surface (different wells or spots) or with the use of unique identifiers/labels (such as spectral separation-different colored dyes, or unique beads-size or color). The strengths and weaknesses of conventional platforms such as immunoassays and new platforms involving protein arrays and lab-on-a-chip technology, including commercially-available devices, are discussed. Three major public health concerns are identified whereby detecting medically-relevant markers using Point-of-Care (POC) multiplex assays could potentially allow for a more efficient diagnosis and treatment of diseases.
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Affiliation(s)
- Samantha Spindel
- Division of Biology, Chemistry, and Materials Science Office of Science and Engineering Laboratories; U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA.
| | - Kim E Sapsford
- Division of Biology, Chemistry, and Materials Science Office of Science and Engineering Laboratories; U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA.
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Lecht S, Gerstenhaber JA, Stabler CT, Pimton P, Karamil S, Marcinkiewicz C, Schulman ES, Lelkes PI. Heterogeneous Mixed-Lineage Differentiation of Mouse Embryonic Stem Cells Induced by Conditioned Media from A549 Cells. Stem Cells Dev 2014; 23:1923-36. [DOI: 10.1089/scd.2014.0042] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Shimon Lecht
- Department of Bioengineering, College of Engineering, Temple University, Philadelphia, Pennsylvania
| | - Jonathan A. Gerstenhaber
- Department of Bioengineering, College of Engineering, Temple University, Philadelphia, Pennsylvania
| | - Collin T. Stabler
- Department of Bioengineering, College of Engineering, Temple University, Philadelphia, Pennsylvania
| | - Pimchanok Pimton
- Department of Biology, School of Science, Walailak University, Thammarat, Thailand
| | - Seda Karamil
- Department of Bioengineering, College of Engineering, Temple University, Philadelphia, Pennsylvania
| | - Cezary Marcinkiewicz
- Department of Bioengineering, College of Engineering, Temple University, Philadelphia, Pennsylvania
| | - Edward S. Schulman
- Division of Pulmonary, Critical Care and Sleep Medicine, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Peter I. Lelkes
- Department of Bioengineering, College of Engineering, Temple University, Philadelphia, Pennsylvania
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15
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Forsberg EM, Sicard C, Brennan JD. Solid-phase biological assays for drug discovery. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2014; 7:337-359. [PMID: 25000820 DOI: 10.1146/annurev-anchem-071213-020241] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In the past 30 years, there has been a significant growth in the use of solid-phase assays in the area of drug discovery, with a range of new assays being used for both soluble and membrane-bound targets. In this review, we provide some basic background to typical drug targets and immobilization protocols used in solid-phase biological assays (SPBAs) for drug discovery, with emphasis on particularly labile biomolecular targets such as kinases and membrane-bound receptors, and highlight some of the more recent approaches for producing protein microarrays, bioaffinity columns, and other devices that are central to small molecule screening by SPBA. We then discuss key applications of such assays to identify drug leads, with an emphasis on the screening of mixtures. We conclude by highlighting specific advantages and potential disadvantages of SPBAs, particularly as they relate to particular assay formats.
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Affiliation(s)
- Erica M Forsberg
- Biointerfaces Institute, McMaster University, Hamilton, Ontario L8S 4L8, Canada;
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16
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Eichelbaum K, Krijgsveld J. Combining pulsed SILAC labeling and click-chemistry for quantitative secretome analysis. Methods Mol Biol 2014; 1174:101-114. [PMID: 24947377 DOI: 10.1007/978-1-4939-0944-5_7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Secreted proteins, such as cytokines, chemokines, and hormones, exhibit central functions in intercellular communication, which is crucial to maintain homeostasis in every multicellular organism. A common approach to identify secreted proteins is by proteomic analysis of culture media after conditioning with a cell type of interest. This is preferably done in serum-free conditions to enable the detection of low-abundance secretory factors that would otherwise be masked by serum proteins. However, serum starvation introduces the risk of bringing cells in a stressed or perturbed state. A superior approach employs the enrichment of newly synthesized and secreted proteins from serum-containing growth medium. This is achieved by the combination of two metabolic labels: stable isotope-labeled amino acids for reliable quantification, and azidohomoalanine (AHA), an azide-bearing analogue of methionine, for the enrichment of newly synthesized and secreted proteins. This approach has been used to compare secretomes of multiple cell lines or to analyze proteins that are secreted upon a specific stimulation. Here we describe in detail the enrichment and quantification of newly synthesized and secreted proteins.
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Affiliation(s)
- Katrin Eichelbaum
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
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Kupcova Skalnikova H. Proteomic techniques for characterisation of mesenchymal stem cell secretome. Biochimie 2013; 95:2196-211. [PMID: 23880644 DOI: 10.1016/j.biochi.2013.07.015] [Citation(s) in RCA: 191] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 07/13/2013] [Indexed: 02/06/2023]
Abstract
Mesenchymal stem cells (MSCs) are multipotent cells with a substantial potential in human regenerative medicine due to their ability to migrate to sites of injury, capability to suppress immune response and accessibility in large amount from patient's own bone marrow or fat tissue. It has been increasingly observed that the transplanted MSCs did not necessarily engraft and differentiate at the site of injury but might exert their therapeutic effects through secreted trophic signals. The MSCs secrete a variety of autocrine/paracrine factors, called secretome, that support regenerative processes in the damaged tissue, induce angiogenesis, protect cells from apoptotic cell death and modulate immune system. The cell culture medium conditioned by MSCs or osteogenic, chondrogenic as well as adipogenic precursors derived from MSCs has become a subject of intensive proteomic profiling in the search for and identification of released factors and microvesicles that might be applicable in regenerative medicine. Jointly with the methods for MSC isolation, expansion and differentiation, proteomic analysis of MSC secretome was enabled recently mainly due to the extensive development in protein separation techniques, mass spectrometry, immunological methods and bioinformatics. This review describes proteomic techniques currently applied or prospectively applicable in MSC secretomics, with a particular focus on preparation of the secretome sample, protein/peptide separation, mass spectrometry and protein quantification techniques, analysis of posttranslational modifications, immunological techniques, isolation and characterisation of secreted vesicles and exosomes, analysis of cytokine-encoding mRNAs and bioinformatics.
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Affiliation(s)
- Helena Kupcova Skalnikova
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, v.v.i., Rumburska 89, 277 21 Libechov, Czech Republic.
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Abdulkareem N, Skroblin P, Jahangiri M, Mayr M. Proteomics in aortic aneurysm - What have we learnt so far? Proteomics Clin Appl 2013; 7:504-15. [DOI: 10.1002/prca.201300016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 02/07/2013] [Accepted: 02/25/2013] [Indexed: 01/14/2023]
Affiliation(s)
- Nada Abdulkareem
- Department of Cardiothoracic Surgery; St. George's Hospital University of London; London UK
| | - Philipp Skroblin
- King's British Heart Foundation Centre; King's College London; London UK
| | - Marjan Jahangiri
- Department of Cardiothoracic Surgery; St. George's Hospital University of London; London UK
| | - Manuel Mayr
- King's British Heart Foundation Centre; King's College London; London UK
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Cell-specific processing and release of the hormone-like precursor and candidate tumor suppressor gene product, Ecrg4. Cell Tissue Res 2012; 348:505-14. [PMID: 22526622 DOI: 10.1007/s00441-012-1396-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 03/05/2012] [Indexed: 01/04/2023]
Abstract
The human open reading frame C2orf40 encodes esophageal cancer-related gene-4 (Ecrg4), a newly recognized neuropeptide-like precursor protein whose gene expression by cells in vitro, over-expression in mice in vivo, and knock-down in zebrafish affects cell proliferation, migration and senescence, progenitor cell survival and differentiation, and inflammatory function. Unlike traditionally secreted neuropeptide precursors, however, we find that Ecrg4 localizes to the epithelial cell surface and remains tethered after secretion. Here, we used cell surface biotinylation to establish that 14-kDa Ecrg4 localizes to the cell surface of prostate (PC3) or kidney (HEK) epithelial cells after transfection. Accordingly, this Ecrg4 is resistant to washing cells with neutral, high salt (2 M NaCl), acidic (50 mM glycine, pH 2.8), or basic (100 mM Na(2)CO(3), pH 11) buffers. Mutagenesis of Ecrg4 established that cell tethering was mediated by an NH(2)-terminus hydrophobic leader sequence that enabled both trafficking to the surface and tethering. Immunoblotting analyses, however, showed that different cells process Ecrg4 differently. Whereas PC3 cells release cell surface Ecrg4 to generate soluble Ecrg4 peptides of 6-14 kDa, HEK cells do neither, and the 14-kDa precursor resembles a sentinel attached to the cell surface. Because a phorbol ester treatment of PC3 cells stimulated Ecrg4 release from, and processing at, the cell surface, these data are consistent with a multifunctional role for Ecrg4 that is dependent on its cell of origin and the molecular form produced.
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