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Juanes-Velasco P, Arias-Hidalgo C, Landeira-Viñuela A, Nuño-Soriano A, Fuentes-Vacas M, Góngora R, Hernández ÁP, Fuentes M. Functional proteomics based on protein microarray technology for biomedical research. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:49-65. [PMID: 38220432 DOI: 10.1016/bs.apcsb.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
This chapter traces a route through Proteomics from its origins to the present day. The different proteomics applications are discussed with a focus on microarray technology. Analytical microarrays, functional microarrays and reverse phase microarrays and their different applications are discussed. Several studies are mentioned where the great versatility of this approach is shown. Finally, the advantages and future challenges of microarray technology are outlined.
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Affiliation(s)
- Pablo Juanes-Velasco
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Carlota Arias-Hidalgo
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Alicia Landeira-Viñuela
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Ana Nuño-Soriano
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Marina Fuentes-Vacas
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Rafa Góngora
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Ángela-Patricia Hernández
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain; Department of Pharmaceutical Sciences: Organic Chemistry, Faculty of Pharmacy, University of Salamanca, CIETUS, IBSAL, Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain; Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain.
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Punetha A, Kotiya D. Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice. Proteomes 2023; 11:2. [PMID: 36648960 PMCID: PMC9844371 DOI: 10.3390/proteomes11010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Proteomics continues to forge significant strides in the discovery of essential biological processes, uncovering valuable information on the identity, global protein abundance, protein modifications, proteoform levels, and signal transduction pathways. Cancer is a complicated and heterogeneous disease, and the onset and progression involve multiple dysregulated proteoforms and their downstream signaling pathways. These are modulated by various factors such as molecular, genetic, tissue, cellular, ethnic/racial, socioeconomic status, environmental, and demographic differences that vary with time. The knowledge of cancer has improved the treatment and clinical management; however, the survival rates have not increased significantly, and cancer remains a major cause of mortality. Oncoproteomics studies help to develop and validate proteomics technologies for routine application in clinical laboratories for (1) diagnostic and prognostic categorization of cancer, (2) real-time monitoring of treatment, (3) assessing drug efficacy and toxicity, (4) therapeutic modulations based on the changes with prognosis and drug resistance, and (5) personalized medication. Investigation of tumor-specific proteomic profiles in conjunction with healthy controls provides crucial information in mechanistic studies on tumorigenesis, metastasis, and drug resistance. This review provides an overview of proteomics technologies that assist the discovery of novel drug targets, biomarkers for early detection, surveillance, prognosis, drug monitoring, and tailoring therapy to the cancer patient. The information gained from such technologies has drastically improved cancer research. We further provide exemplars from recent oncoproteomics applications in the discovery of biomarkers in various cancers, drug discovery, and clinical treatment. Overall, the future of oncoproteomics holds enormous potential for translating technologies from the bench to the bedside.
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Affiliation(s)
- Ankita Punetha
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers University, 225 Warren St., Newark, NJ 07103, USA
| | - Deepak Kotiya
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, 900 South Limestone St., Lexington, KY 40536, USA
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Abstract
Articular cartilage is a unique load-bearing connective tissue with a low intrinsic capacity for repair and regeneration. Its avascularity makes it relatively hypoxic and its unique extracellular matrix is enriched with cations, which increases the interstitial fluid osmolarity. Several physicochemical and biomechanical stimuli are reported to influence chondrocyte metabolism and may be utilized for regenerative medical approaches. In this review article, we summarize the most relevant stimuli and describe how ion channels may contribute to cartilage homeostasis, with special emphasis on intracellular signaling pathways. We specifically focus on the role of calcium signaling as an essential mechanotransduction component and highlight the role of phosphatase signaling in this context.
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Affiliation(s)
- Holger Jahr
- Department of Orthopaedic Surgery, University Hospital RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany
- The D-BOARD European Consortium for Biomarker Discovery, Surrey, UK
| | - Csaba Matta
- The D-BOARD European Consortium for Biomarker Discovery, Surrey, UK
- Department of Veterinary Preclinical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Duke of Kent Building, Guildford, Surrey GU2 7XH UK
- Department of Anatomy, Histology and Embryology, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, 4032 Hungary
| | - Ali Mobasheri
- The D-BOARD European Consortium for Biomarker Discovery, Surrey, UK
- Department of Veterinary Preclinical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Duke of Kent Building, Guildford, Surrey GU2 7XH UK
- Arthritis Research UK Centre for Sport, Exercise and Osteoarthritis, Arthritis Research UK Pain Centre, Medical Research Council and Arthritis Research UK Centre for Musculoskeletal Ageing Research, University of Nottingham, Queen’s Medical Centre, Nottingham, NG7 2UH UK
- Center of Excellence in Genomic Medicine Research (CEGMR), King Fahd Medical Research Center (KFMRC), King AbdulAziz University, Jeddah, 21589 Kingdom of Saudi Arabia
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Abstract
Tissue engineering holds promise for the treatment of damaged and diseased tissues, especially for those tissues that do not undergo repair and regeneration readily in situ. Many techniques are available for cell and tissue culturing and differentiation of chondrocytes using a variety of cell types, differentiation methods, and scaffolds. In each case, it is critical to demonstrate the cellular phenotype and tissue composition, with particular attention to the extracellular matrix molecules that play a structural role and that contribute to the mechanical properties of the resulting tissue construct. Mass spectrometry provides an ideal analytical method with which to characterize the full spectrum of proteins produced by tissue-engineered cartilage. Using normal cartilage tissue as a standard, tissue-engineered cartilage can be optimized according to the entire proteome. Proteomic analysis is a complementary approach to biochemical, immunohistochemical, and mechanical testing of cartilage constructs. Proteomics is applicable as an analysis approach to most cartilage constructs generated from a variety of cellular sources including primary chondrocytes, mesenchymal stem cells from bone marrow, adipose tissue, induced pluripotent stem cells, and embryonic stem cells. Additionally, proteomics can be used to optimize novel scaffolds and bioreactor applications, yielding cartilage tissue with the proteomic profile of natural cartilage.
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Affiliation(s)
- Xinzhu Pu
- Department of Biological Sciences, Biomolecular Research Center, Boise State University, Boise, ID, USA
| | - Julia Thom Oxford
- Department of Biological Sciences, Biomolecular Research Center, Boise State University, 1910 University Drive, Mail Stop 1511, Boise, ID, USA.
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Mesri M. Advances in Proteomic Technologies and Its Contribution to the Field of Cancer. Adv Med 2014; 2014:238045. [PMID: 26556407 PMCID: PMC4590950 DOI: 10.1155/2014/238045] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 06/30/2014] [Indexed: 12/12/2022] Open
Abstract
Systematic studies of the cancer genome have generated a wealth of knowledge in recent years. These studies have uncovered a number of new cancer genes not previously known to be causal targets in cancer. Genetic markers can be used to determine predisposition to tumor development, but molecularly targeted treatment strategies are not widely available for most cancers. Precision care plans still must be developed by understanding and implementing basic science research into clinical treatment. Proteomics is continuing to make major strides in the discovery of fundamental biological processes as well as more recent transition into an assay platform capable of measuring hundreds of proteins in any biological system. As such, proteomics can translate basic science discoveries into the clinical practice of precision medicine. The proteomic field has progressed at a fast rate over the past five years in technology, breadth and depth of applications in all areas of the bioscience. Some of the previously experimental technical approaches are considered the gold standard today, and the community is now trying to come to terms with the volume and complexity of the data generated. Here I describe contribution of proteomics in general and biological mass spectrometry in particular to cancer research, as well as related major technical and conceptual developments in the field.
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Affiliation(s)
- Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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Rocha B, Calamia V, Casas V, Carrascal M, Blanco FJ, Ruiz-Romero C. Secretome Analysis of Human Mesenchymal Stem Cells Undergoing Chondrogenic Differentiation. J Proteome Res 2014; 13:1045-54. [DOI: 10.1021/pr401030n] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Beatriz Rocha
- Rheumatology Division,
ProteoRed/ISCIII Proteomics Group, INIBIC—Hospital Universitario
de A Coruña, C/Xubias 84, 15006-A Coruña, Spain
| | - Valentina Calamia
- Rheumatology Division,
ProteoRed/ISCIII Proteomics Group, INIBIC—Hospital Universitario
de A Coruña, C/Xubias 84, 15006-A Coruña, Spain
| | - Vanessa Casas
- CSIC/UAB Proteomics
Laboratory, Instituto de Investigaciones Biomédicas de Barcelona-Consejo
Superior de Investigaciones Científicas, 08193-Bellaterra, Spain
| | - Montserrat Carrascal
- CSIC/UAB Proteomics
Laboratory, Instituto de Investigaciones Biomédicas de Barcelona-Consejo
Superior de Investigaciones Científicas, 08193-Bellaterra, Spain
| | - Francisco J. Blanco
- Rheumatology Division,
ProteoRed/ISCIII Proteomics Group, INIBIC—Hospital Universitario
de A Coruña, C/Xubias 84, 15006-A Coruña, Spain
- RIER-RED
de Inflamación
y Enfermedades Reumáticas, INIBIC−CHUAC, 15006-A Coruña, Spain
| | - Cristina Ruiz-Romero
- Rheumatology Division,
ProteoRed/ISCIII Proteomics Group, INIBIC—Hospital Universitario
de A Coruña, C/Xubias 84, 15006-A Coruña, Spain
- CIBER-BBN Instituto
de Salud Carlos III, INIBIC−CHUAC, 15006-A Coruña, Spain
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Oswald ES, Brown LM, Bulinski JC, Hung CT. Label-free protein profiling of adipose-derived human stem cells under hyperosmotic treatment. J Proteome Res 2011; 10:3050-9. [PMID: 21604804 DOI: 10.1021/pr200030v] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Our previous work suggested that treatment of cells with hyperosmotic media during 2D passaging primes cells for cartilage tissue engineering applications. Here, we used label-free proteomic profiling to evaluate the effects of control and hyperosmotic treatment environments on the phenotype of multipotent adipose-derived stem cells (ASCs) cultivated with a chondrogenic growth factor cocktail. Spectra were recorded in a data-independent fashion at alternate low (precursor) and high (product) fragmentation voltages (MS(E)). This method was supplemented with data mining of accurate mass and retention time matches in precursor ion spectra across the experiment. The results indicated a complex cellular response to osmotic treatment, with a number of proteins differentially expressed between control and treated cell groups. The roles of some of these proteins have been documented in the literature as characteristic of the physiological states studied, especially aldose reductase (osmotic stress). This protein acted as a positive control in this work, providing independent corroborative validation. Other proteins, including 5'-nucleotidase and transgelin, have been previously linked to cell differentiation state. This study demonstrates that label-free profiling can serve as a useful tool in characterizing cellular responses to chondrogenic treatment regimes, recommending its use in optimization of cell priming protocols for cartilage tissue engineering.
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Affiliation(s)
- Elizabeth S Oswald
- Department of Biomedical Engineering, Columbia University, New York, New York, USA
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Sokolowska I, Woods AG, Wagner J, Dorler J, Wormwood K, Thome J, Darie CC. Mass Spectrometry for Proteomics-Based Investigation of Oxidative Stress and Heat Shock Proteins. ACS SYMPOSIUM SERIES 2011. [DOI: 10.1021/bk-2011-1083.ch013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Izabela Sokolowska
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810, U.S.A
- Department of Psychiatry, University of Rostock, Gehlsheimer Straße 20, D-18147 Rostock, Germany
| | - Alisa G. Woods
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810, U.S.A
- Department of Psychiatry, University of Rostock, Gehlsheimer Straße 20, D-18147 Rostock, Germany
| | - Jessica Wagner
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810, U.S.A
- Department of Psychiatry, University of Rostock, Gehlsheimer Straße 20, D-18147 Rostock, Germany
| | - Jeannette Dorler
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810, U.S.A
- Department of Psychiatry, University of Rostock, Gehlsheimer Straße 20, D-18147 Rostock, Germany
| | - Kelly Wormwood
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810, U.S.A
- Department of Psychiatry, University of Rostock, Gehlsheimer Straße 20, D-18147 Rostock, Germany
| | - Johannes Thome
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810, U.S.A
- Department of Psychiatry, University of Rostock, Gehlsheimer Straße 20, D-18147 Rostock, Germany
| | - Costel C. Darie
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810, U.S.A
- Department of Psychiatry, University of Rostock, Gehlsheimer Straße 20, D-18147 Rostock, Germany
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