1
|
Proteomic Exploration of Plasma Exosomes and Other Small Extracellular Vesicles in Pediatric Hodgkin Lymphoma: A Potential Source of Biomarkers for Relapse Occurrence. Diagnostics (Basel) 2021; 11:diagnostics11060917. [PMID: 34063765 PMCID: PMC8223799 DOI: 10.3390/diagnostics11060917] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/14/2021] [Accepted: 05/19/2021] [Indexed: 12/22/2022] Open
Abstract
Exosomes and other small extracellular vesicles (EVs) are potential sources of cancer biomarkers. Plasma-derived EVs have not yet been studied in pediatric Hodgkin lymphoma (HL), for which predictive biomarkers of relapse are greatly needed. In this two-part proteomic study, we used two-dimensional difference gel electrophoresis (2D-DIGE) followed by liquid chromatography–tandem mass spectrometry (LC–MS/MS) to analyze EV proteins of plasma collected at diagnosis from children with nodular sclerosis HL, relapsed or not. EVs isolated using membrane affinity had radii ranging from 20 to 130 nm and contained the programmed cell death 6-interacting (ALIX) and the tumor susceptibility gene 101 (TSG101) proteins, whereas calnexin (CANX) was not detected. 2D-DIGE identified 16 spots as differentially abundant between non-relapsed and relapsed HL (|fold change| ≥ 1.5, p < 0.05). LC–MS/MS identified these spots as 11 unique proteins, including five more abundant in non-relapsed HL (e.g., complement C4b, C4B; fibrinogen γ chain, FGG) and six more abundant in relapsed HL (e.g., transthyretin, TTR). Shotgun LC–MS/MS on pooled EV proteins from non-relapsed HL identified 161 proteins, including 127 already identified in human exosomes (ExoCarta data). This EV cargo included 89 proteins not yet identified in exosomes from healthy plasma. Functional interrogation by the Database for Annotation, Visualization and Integrated Discovery (DAVID) revealed that the EV proteins participate in platelet degranulation and serine-type endopeptidase activity as the most significant Gene Ontology (GO) biological process and molecular function (p < 0.01).
Collapse
|
2
|
Morsbach S, Gonella G, Mailänder V, Wegner S, Wu S, Weidner T, Berger R, Koynov K, Vollmer D, Encinas N, Kuan SL, Bereau T, Kremer K, Weil T, Bonn M, Butt HJ, Landfester K. Engineering von Proteinen an Oberflächen: Von komplementärer Charakterisierung zu Materialoberflächen mit maßgeschneiderten Funktionen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712448] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Svenja Morsbach
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Grazia Gonella
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Volker Mailänder
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
- Abteilung für Dermatologie; Universitätsmedizin der Johannes Gutenberg-Universität Mainz; Langenbeckstraße 1 55131 Mainz Deutschland
| | - Seraphine Wegner
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Si Wu
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Tobias Weidner
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
- Abteilung für Chemie; Universität Aarhus; Langelandsgade 140 8000 Aarhus C Dänemark
| | - Rüdiger Berger
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Kaloian Koynov
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Doris Vollmer
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Noemí Encinas
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Seah Ling Kuan
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Tristan Bereau
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Kurt Kremer
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Tanja Weil
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Mischa Bonn
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Hans-Jürgen Butt
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Katharina Landfester
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| |
Collapse
|
3
|
Morsbach S, Gonella G, Mailänder V, Wegner S, Wu S, Weidner T, Berger R, Koynov K, Vollmer D, Encinas N, Kuan SL, Bereau T, Kremer K, Weil T, Bonn M, Butt HJ, Landfester K. Engineering Proteins at Interfaces: From Complementary Characterization to Material Surfaces with Designed Functions. Angew Chem Int Ed Engl 2018; 57:12626-12648. [PMID: 29663610 PMCID: PMC6391961 DOI: 10.1002/anie.201712448] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/13/2018] [Indexed: 01/17/2023]
Abstract
Once materials come into contact with a biological fluid containing proteins, proteins are generally—whether desired or not—attracted by the material's surface and adsorb onto it. The aim of this Review is to give an overview of the most commonly used characterization methods employed to gain a better understanding of the adsorption processes on either planar or curved surfaces. We continue to illustrate the benefit of combining different methods to different surface geometries of the material. The thus obtained insight ideally paves the way for engineering functional materials that interact with proteins in a predetermined manner.
Collapse
Affiliation(s)
- Svenja Morsbach
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Grazia Gonella
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Volker Mailänder
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.,Department of Dermatology, University Medical Center Johannes Gutenberg-University Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Seraphine Wegner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Si Wu
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tobias Weidner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.,Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Rüdiger Berger
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Kaloian Koynov
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Doris Vollmer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Noemí Encinas
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Seah Ling Kuan
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tanja Weil
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Hans-Jürgen Butt
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Katharina Landfester
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| |
Collapse
|
4
|
Taniguchi M, Kameda M, Namae T, Ochiai A, Saitoh E, Tanaka T. Identification and characterization of multifunctional cationic peptides derived from peptic hydrolysates of rice bran protein. J Funct Foods 2017. [DOI: 10.1016/j.jff.2017.04.046] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
|
5
|
Koirala D, Mistry S, Wenthold PG. Participation of C-H Protons in the Dissociation of a Proton Deficient Dipeptide. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1313-1323. [PMID: 28429299 DOI: 10.1007/s13361-017-1662-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 03/13/2017] [Accepted: 03/14/2017] [Indexed: 06/07/2023]
Abstract
The dissociation of anionic dipeptides Phe*Gly and GlyPhe*, where Phe* refers to sulfonated phenyl alanine, has been investigated by using ion trap mass spectrometry. The dipeptides undergo collision-induced dissociation (CID) to give the same products, indicating that they rearrange to a common structure before dissociation. The rearrangement does not occur with the dipeptide methyl esters. The structures of the b2 ions were investigated to determine the effect that having a remote, anionic site has on product formation. Comparison with the CID spectra for authentic structures shows that the b2 ion obtained from GlyPhe* has predominantly a diketopiperazine structure. The CID spectra for the Phe*Gly b2 ion and the authentic oxazolone are similar, but differences in intensity suggest a two-component mixture. Isotopic labeling studies are consistent with the formation of two products, with one resulting from loss of a non-mobile proton on the Gly α-carbon. The results are attributed to the formation of an oxazole and oxazolone enol product. Electronic structure calculations predict that the enol structure of the Phe*Gly b2 ion is lower in energy than the keto version due to intramolecular hydrogen bonding with the sulfonate group. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Damodar Koirala
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47906, USA
| | - Sabyasachy Mistry
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47906, USA
| | - Paul G Wenthold
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47906, USA.
| |
Collapse
|
6
|
Ochiai A, Tanaka S, Tanaka T, Taniguchi M. Rice Bran Protein as a Potent Source of Antimelanogenic Peptides with Tyrosinase Inhibitory Activity. JOURNAL OF NATURAL PRODUCTS 2016; 79:2545-2551. [PMID: 27648609 DOI: 10.1021/acs.jnatprod.6b00449] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Rice (Oryza sativa) is consumed as a staple food globally, and rice bran, the byproduct, is an unused biomass that is ultimately discarded as waste. Thus, in the present study, a technique for producing tyrosinase inhibitory peptides from rice bran protein (RBP) was developed. Simultaneous treatment of RBP with chymotrypsin and trypsin produced numerous peptides. Subsequently, six tyrosinase inhibitory peptides were isolated from the hydrolysate fractions in a multistep purification protocol, and their amino acid sequences were determined. Three of these peptides had a C-terminal tyrosine residue and exhibited significant inhibitory effects against tyrosinase-mediated monophenolase reactions. Furthermore, peptide CT-2 (Leu-Gln-Pro-Ser-His-Tyr) potently inhibited melanogenesis in mouse B16 melanoma cells without causing cytotoxicity, suggesting the potential of CT-2 as an agent for melanin-related skin disorder treatment. The present data indicate that RBP is a potent source of tyrosinase inhibitory peptides and that simultaneous treatment of RBP with chymotrypsin and trypsin efficiently produces these peptides.
Collapse
Affiliation(s)
- Akihito Ochiai
- Department of Materials Science and Technology, Faculty of Engineering, and ‡Graduate School of Science and Technology, Niigata University , Niigata 950-2181, Japan
| | - Seiya Tanaka
- Department of Materials Science and Technology, Faculty of Engineering, and ‡Graduate School of Science and Technology, Niigata University , Niigata 950-2181, Japan
| | - Takaaki Tanaka
- Department of Materials Science and Technology, Faculty of Engineering, and ‡Graduate School of Science and Technology, Niigata University , Niigata 950-2181, Japan
| | - Masayuki Taniguchi
- Department of Materials Science and Technology, Faculty of Engineering, and ‡Graduate School of Science and Technology, Niigata University , Niigata 950-2181, Japan
| |
Collapse
|
7
|
Cassagne C, Normand AC, L'Ollivier C, Ranque S, Piarroux R. Performance of MALDI-TOF MS platforms for fungal identification. Mycoses 2016; 59:678-690. [DOI: 10.1111/myc.12506] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 03/04/2016] [Accepted: 03/12/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Carole Cassagne
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
- Aix-Marseille University; UMR MD3 IP-TPT; Marseilles France
| | - Anne-Cécile Normand
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
| | - Coralie L'Ollivier
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
- Aix-Marseille University; UMR MD3 IP-TPT; Marseilles France
| | - Stéphane Ranque
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
- Aix-Marseille University; UMR MD3 IP-TPT; Marseilles France
| | - Renaud Piarroux
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
- Aix-Marseille University; UMR MD3 IP-TPT; Marseilles France
| |
Collapse
|
8
|
Abstract
Proteomics and biochemical profiling have emerged as exciting and powerful tools in clinical biomarker research. In the field of transplantation, proteomics aims not only at developing noninvasive means for immune monitoring but also to gain mechanistic insights into the pathophysiology of the alloimmune response and hence defining new therapeutic targets. This chapter provides an overview of proteomic biomarker-driven approaches and its underlying concepts and discusses the advantages, clinical implications, challenges, and limitations of this novel modality as it relates to solid organ transplantation.
Collapse
Affiliation(s)
- Katrin Kienzl-Wagner
- Center of Operative Medicine, Department of Visceral, Transplant and Thoracic Surgery, Innsbruck Medical University, Innsbruck, Austria
| | - Gerald Brandacher
- Department of Plastic and Reconstructive Surgery, Vascularized Composite Allotransplantation (VCA) Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
| |
Collapse
|
9
|
Lin SY, Hsu WH, Lin CC, Chen CJ. Mass spectrometry-based proteomics in Chest Medicine, Gerontology, and Nephrology: subgroups omics for personalized medicine. Biomedicine (Taipei) 2014; 4:25. [PMID: 25520938 PMCID: PMC4264973 DOI: 10.7603/s40681-014-0025-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 07/30/2014] [Indexed: 12/12/2022] Open
Abstract
Mass spectrometry (MS) is currently the most promising tool for studying proteomics to investigate largescale proteins in a specific proteome. Emerging MS-based proteomics is widely applied to decipher complex proteome for discovering potential biomarkers. Given its growing usage in clinical medicine for biomarker discovery to predict, diagnose and confer prognosis, MS-based proteomics can benefit study of personalized medicine. In this review we introduce some fundamental MS theory and MS-based quantitative proteomic approaches as well as several representative clinical MS-based proteomics issues in Chest Medicine, Gerontology, and Nephrology.
Collapse
Affiliation(s)
- Shih-Yi Lin
- Institute of Clinical Medical Science, China Medical University College of Medicine, 404 Taichung, Taiwan
- Department of Internal Medicine, China Medical University Hospital, 404 Taichung, Taiwan
- Division of Nephrology and Kidney Institute, China Medical University Hospital, 404 Taichung, Taiwan
| | - Wu-Huei Hsu
- Institute of Clinical Medical Science, China Medical University College of Medicine, 404 Taichung, Taiwan
- Department of Internal Medicine, China Medical University Hospital, 404 Taichung, Taiwan
- Division of Pulmonary and Critical Care Medicine, China Medical University Hospital and China Medical University, 404 Taichung, Taiwan
| | - Cheng-Chieh Lin
- Institute of Clinical Medical Science, China Medical University College of Medicine, 404 Taichung, Taiwan
- Department of Family Medicine, China Medical University Hospital, 404 Taichung, Taiwan
- School of Medicine, College of Medicine China Medical University, No. 91, Hsueh Shih Road, 404 Taichung, Taiwan
| | - Chao-Jung Chen
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, No. 91, Hsueh-Shih Road, 402 Taichung, Taiwan
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, 404 Taichung, Taiwan
| |
Collapse
|
10
|
Hall MP. Biotransformation and in vivo stability of protein biotherapeutics: impact on candidate selection and pharmacokinetic profiling. Drug Metab Dispos 2014; 42:1873-80. [PMID: 24947971 DOI: 10.1124/dmd.114.058347] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Historically, since the metabolism of administered peptide/protein drugs ("biotherapeutics") has been expected to undergo predictable pathways similar to endogenous proteins, comprehensive biotherapeutic metabolism studies have not been widely reported in the literature. However, since biotherapeutics have rapidly evolved into an impressive array of eclectic modalities, there has been a shift toward understanding the impact of metabolism on biotherapeutic development. For biotherapeutics containing non-native chemical linkers and other moieties besides natural amino acids, metabolism studies are critical as these moieties may impart undesired toxicology. For biotherapeutics that are composed solely of natural amino acids, where end-stage peptide and amino acid catabolites do not generally pose toxicity concerns, the understanding of biotherapeutic biotransformation, defined as in vivo modifications such as peripherally generated intermediate circulating catabolites prior to end-stage degradation or elimination, may impact in vivo stability and potency/clearance. As of yet, there are no harmonized methodologies for understanding biotherapeutic biotransformation and its impact on drug development, nor is there clear guidance from regulatory agencies on how and when these studies should be conducted. This review provides an update on biotherapeutic biotransformation studies and an overview of lessons learned, tools that have been developed, and suggestions of approaches to address issues. Biotherapeutic biotransformation studies, especially for certain modalities, should be implemented at an early stage of development to 1) understand the impact on potency/clearance, 2) select the most stable candidates or direct protein re-engineering efforts, and 3) select the best bioanalytical technique(s) for proper drug quantification and subsequent pharmacokinetic profiling and exposure/response assessment.
Collapse
Affiliation(s)
- Michael P Hall
- Department of Pharmacokinetics & Drug Metabolism, Amgen Inc., Thousand Oaks, California
| |
Collapse
|
11
|
Ahmed FE. Utility of mass spectrometry for proteome analysis: part II. Ion-activation methods, statistics, bioinformatics and annotation. Expert Rev Proteomics 2014; 6:171-97. [DOI: 10.1586/epr.09.4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
12
|
Biomarker discovery in transplantation—proteomic adventure or mission impossible? Clin Biochem 2013; 46:497-505. [DOI: 10.1016/j.clinbiochem.2012.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/09/2012] [Accepted: 10/11/2012] [Indexed: 01/10/2023]
|
13
|
Ochiai A, Harada K, Hashimoto K, Shibata K, Ishiyama Y, Mitsui T, Tanaka T, Taniguchi M. α-Amylase is a potential growth inhibitor of Porphyromonas gingivalis
, a periodontal pathogenic bacterium. J Periodontal Res 2013; 49:62-8. [DOI: 10.1111/jre.12079] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2013] [Indexed: 12/19/2022]
Affiliation(s)
- A. Ochiai
- Department of Materials Science and Technology; Faculty of Engineering; Niigata University; Niigata Japan
| | - K. Harada
- Department of Materials Science and Technology; Faculty of Engineering; Niigata University; Niigata Japan
| | - K. Hashimoto
- Department of Materials Science and Technology; Faculty of Engineering; Niigata University; Niigata Japan
| | - K. Shibata
- Department of Materials Science and Technology; Faculty of Engineering; Niigata University; Niigata Japan
| | - Y. Ishiyama
- Department of Materials Science and Technology; Faculty of Engineering; Niigata University; Niigata Japan
| | - T. Mitsui
- Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Niigata Japan
| | - T. Tanaka
- Department of Materials Science and Technology; Faculty of Engineering; Niigata University; Niigata Japan
| | - M. Taniguchi
- Department of Materials Science and Technology; Faculty of Engineering; Niigata University; Niigata Japan
| |
Collapse
|
14
|
Serum biomarkers identification by mass spectrometry in high-mortality tumors. INTERNATIONAL JOURNAL OF PROTEOMICS 2013; 2013:125858. [PMID: 23401773 PMCID: PMC3562576 DOI: 10.1155/2013/125858] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 11/16/2012] [Accepted: 12/11/2012] [Indexed: 02/08/2023]
Abstract
Cancer affects millions of people worldwide. Tumor mortality is substantially due to diagnosis at stages that are too late for therapies to be effective. Advances in screening methods have improved the early diagnosis, prognosis, and survival for some cancers. Several validated biomarkers are currently used to diagnose and monitor the progression of cancer, but none of them shows adequate specificity, sensitivity, and predictive value for population screening. So, there is an urgent need to isolate novel sensitive, specific biomarkers to detect the disease early and improve prognosis, especially in high-mortality tumors. Proteomic techniques are powerful tools to help in diagnosis and monitoring of treatment and progression of the disease. During the last decade, mass spectrometry has assumed a key role in most of the proteomic analyses that are focused on identifying cancer biomarkers in human serum, making it possible to identify and characterize at the molecular level many proteins or peptides differentially expressed. In this paper we summarize the results of mass spectrometry serum profiling and biomarker identification in high mortality tumors, such as ovarian, liver, lung, and pancreatic cancer.
Collapse
|
15
|
Zybailov BL, Glazko GV, Jaiswal M, Raney KD. Large Scale Chemical Cross-linking Mass Spectrometry Perspectives. ACTA ACUST UNITED AC 2013; 6:001. [PMID: 25045217 PMCID: PMC4101816 DOI: 10.4172/jpb.s2-001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The spectacular heterogeneity of a complex protein mixture from biological samples becomes even more difficult to tackle when one’s attention is shifted towards different protein complex topologies, transient interactions, or localization of PPIs. Meticulous protein-by-protein affinity pull-downs and yeast-two-hybrid screens are the two approaches currently used to decipher proteome-wide interaction networks. Another method is to employ chemical cross-linking, which gives not only identities of interactors, but could also provide information on the sites of interactions and interaction interfaces. Despite significant advances in mass spectrometry instrumentation over the last decade, mapping Protein-Protein Interactions (PPIs) using chemical cross-linking remains time consuming and requires substantial expertise, even in the simplest of systems. While robust methodologies and software exist for the analysis of binary PPIs and also for the single protein structure refinement using cross-linking-derived constraints, undertaking a proteome-wide cross-linking study is highly complex. Difficulties include i) identifying cross-linkers of the right length and selectivity that could capture interactions of interest; ii) enrichment of the cross-linked species; iii) identification and validation of the cross-linked peptides and cross-linked sites. In this review we examine existing literature aimed at the large-scale protein cross-linking and discuss possible paths for improvement. We also discuss short-length cross-linkers of broad specificity such as formaldehyde and diazirine-based photo-cross-linkers. These cross-linkers could potentially capture many types of interactions, without strict requirement for a particular amino-acid to be present at a given protein-protein interface. How these shortlength, broad specificity cross-linkers be applied to proteome-wide studies? We will suggest specific advances in methodology, instrumentation and software that are needed to make such a leap.
Collapse
Affiliation(s)
- Boris L Zybailov
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Galina V Glazko
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Mihir Jaiswal
- UALR/UAMS Joint Bioinformatics Program, University of Arkansas Little Rock, Little Rock, AR, USA
| | - Kevin D Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| |
Collapse
|
16
|
Lin Y, Jiang H, Yan Y, Peng B, Chen J, Lin H, Liu Z. Shotgun analysis of membrane proteomes by an improved SDS-assisted sample preparation method coupled with liquid chromatography–tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 911:6-14. [DOI: 10.1016/j.jchromb.2012.10.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 10/14/2012] [Accepted: 10/15/2012] [Indexed: 10/27/2022]
|
17
|
Breitkopf SB, Asara JM. Determining in vivo phosphorylation sites using mass spectrometry. ACTA ACUST UNITED AC 2012; Chapter 18:Unit18.19.1-27. [PMID: 22470061 DOI: 10.1002/0471142727.mb1819s98] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Phosphorylation is the most studied protein post-translational modification (PTM) in biological systems, since it controls cell growth, proliferation, survival, and other processes. High-resolution/high mass accuracy mass spectrometers are used to identify protein phosphorylation sites due to their speed, sensitivity, selectivity, and throughput. The protocols described here focus on two common strategies: (1) identifying phosphorylation sites from individual proteins and small protein complexes, and (2) identifying global phosphorylation sites from whole-cell and tissue extracts. For the first, endogenous or epitope-tagged proteins are typically immunopurified from cell lysates, purified via gel electrophoresis or precipitation, and enzymatically digested into peptides. Samples can be optionally enriched for phosphopeptides using immobilized metal affinity chromatography (IMAC) or titanium dioxide (TiO(2)) and then analyzed by microcapillary liquid chromatography/tandem mass spectrometry (LC-MS/MS). Global phosphorylation site analyses that capture pSer/pThr/pTyr sites from biological sources sites are more resource and time consuming and involve digesting the whole-cell lysate, followed by peptide fractionation by strong cation-exchange chromatography, phosphopeptide enrichment by IMAC or TiO(2), and LC-MS/MS. Alternatively, the protein lysate can be fractionated by SDS-PAGE, followed by digestion, phosphopeptide enrichment, and LC-MS/MS. One can also immunoprecipitate only phosphotyrosine peptides using a pTyr antibody followed by LC-MS/MS.
Collapse
Affiliation(s)
- Susanne B Breitkopf
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | | |
Collapse
|
18
|
Zhou J, Hu Y, Lin Y, Liu H, Xie P. Preparation and application of a partially degradable gel in mass spectrometry-based proteomic analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:2957-62. [DOI: 10.1016/j.jchromb.2011.08.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 08/13/2011] [Accepted: 08/15/2011] [Indexed: 10/17/2022]
|
19
|
Thirant C, Varlet P, Lipecka J, Le Gall M, Broussard C, Chafey P, Studler JM, Lacombe J, Lions S, Guillaudeau A, Camoin L, Daumas-Duport C, Junier MP, Chneiweiss H. Proteomic analysis of oligodendrogliomas expressing a mutant isocitrate dehydrogenase-1. Proteomics 2011; 11:4139-54. [DOI: 10.1002/pmic.201000646] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 07/19/2011] [Accepted: 08/04/2011] [Indexed: 12/17/2022]
|
20
|
Proteomics—A Blessing or a Curse? Application of Proteomics Technology to Transplant Medicine. Transplantation 2011; 92:499-509. [DOI: 10.1097/tp.0b013e3182265358] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
21
|
Macek B, Mijakovic I. Site-specific analysis of bacterial phosphoproteomes. Proteomics 2011; 11:3002-11. [PMID: 21726046 DOI: 10.1002/pmic.201100012] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2011] [Revised: 03/05/2011] [Accepted: 03/08/2011] [Indexed: 11/11/2022]
Abstract
Protein phosphorylation on serine, threonine and tyrosine is established as an important regulatory modification in bacteria. A growing number of studies employing mass spectrometry-based proteomics report large protein phosphorylation datasets, providing precise evidence for in-vivo phosphorylation that is especially suitable for functional follow-up. Here, we provide an overview of the strategies currently used in bacterial phosphoproteomics, with an emphasis on gel-free proteomics and approaches that enable global detection of phosphorylation sites in bacterial proteins. The proteomics technology has matured sufficiently to permit routine characterization of phosphoproteomes and phosphopeptides with high sensitivity; we argue that the next challenge in the field will be the large-scale detection of protein kinase and phosphatase substrates and their integration into regulatory networks of the bacterial cell.
Collapse
Affiliation(s)
- Boris Macek
- Proteome Center Tuebingen, University of Tuebingen, Germany.
| | | |
Collapse
|
22
|
Abstract
Organs are complex structures that consist of multiple tissues with different levels of gene expression. To achieve comprehensive coverage and accurate quantitation data, organs ideally should be separated into morphologic and/or functional substructures before gene or protein expression analysis. However, because of complex morphology and elaborate isolation protocols, to date this often has been difficult to achieve. Kidneys are organs in which functional and morphologic subdivision is especially important. Each subunit of the kidney, the nephron, consists of more than 10 subsegments with distinct morphologic and functional characteristics. For a full understanding of kidney physiology, global gene and protein expression analyses have to be performed at the level of the nephron subsegments; however, such studies have been extremely rare to date. Here we describe the latest approaches in quantitative high-accuracy mass spectrometry-based proteomics and their application to quantitative proteomics studies of the whole kidney and nephron subsegments, both in human beings and in animal models. We compare these studies with similar studies performed on other organ substructures. We argue that the newest technologies used for preparation, processing, and measurement of small amounts of starting material are finally enabling global and subsegment-specific quantitative measurement of protein levels in the kidney and other organs. These new technologies and approaches are making a decisive impact on our understanding of the (patho)physiological processes at the molecular level.
Collapse
|
23
|
Martins-de-Souza D, Guest PC, Vanattou-Saifoudine N, Harris LW, Bahn S. Proteomic technologies for biomarker studies in psychiatry: advances and needs. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2011; 101:65-94. [PMID: 22050849 DOI: 10.1016/b978-0-12-387718-5.00004-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In the postgenome era, proteomics has arisen as a promising tool for more complete comprehension of diseases and for biomarker discovery. Some of these objectives have already been partly achieved for illnesses such as cancer. In the case of psychiatric conditions, however, proteomic advances have had a less profound impact. Here, we outline the necessity of improving and applying proteomic methods for biomarker discovery and validation in the field of psychiatric disorders. While proteomic-based applications in neurosciences have increased in accuracy and sensitivity over the past 10 years, the development of orthogonal validation technologies has fallen behind. These issues are discussed along with the importance of integrating systems biology approaches and combining proteomics with other research approaches. The future development of such technologies may put proteomics closer to clinical applications in psychiatry.
Collapse
Affiliation(s)
- Daniel Martins-de-Souza
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | | | | | | | | |
Collapse
|
24
|
Rahbar A, Rivers R, Boja E, Kinsinger C, Mesri M, Hiltke T, Rodriguez H. Realizing individualized medicine: the road to translating proteomics from the laboratory to the clinic. Per Med 2011; 8:45-57. [DOI: 10.2217/pme.10.76] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The sequencing of the human genome has brought great promise and potential for the future of medicine, as well as providing a strong momentum for the burgeoning field of individualized medicine. Tests based on genetic information can be used to allow physicians to target therapies for those patients most likely to benefit from specific therapies and identify potential risk before the onset of disease. While advances in genomics-based molecular diagnostics are progressing, producing some useful US FDA-approved/-cleared diagnostic tests, protein-based molecular diagnostics have not met its promised potential. This article will provide an overview of protein-based analysis technologies, identify their strengths and limitations, discuss barriers to protein-based biomarker development and identify issues which must be addressed in order to successfully transfer the field of proteomics from the laboratory to the clinic.
Collapse
Affiliation(s)
- Amir Rahbar
- Office of Cancer Clinical Proteomics Research, Center for Strategic Scientific Initiatives, National Cancer Institute, National Institutes of Health, 31 Center Drive, Bethesda, MD 20892, USA
| | - Robert Rivers
- Office of Cancer Clinical Proteomics Research, Center for Strategic Scientific Initiatives, National Cancer Institute, National Institutes of Health, 31 Center Drive, Bethesda, MD 20892, USA
| | - Emily Boja
- Office of Cancer Clinical Proteomics Research, Center for Strategic Scientific Initiatives, National Cancer Institute, National Institutes of Health, 31 Center Drive, Bethesda, MD 20892, USA
| | - Christopher Kinsinger
- Office of Cancer Clinical Proteomics Research, Center for Strategic Scientific Initiatives, National Cancer Institute, National Institutes of Health, 31 Center Drive, Bethesda, MD 20892, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, Center for Strategic Scientific Initiatives, National Cancer Institute, National Institutes of Health, 31 Center Drive, Bethesda, MD 20892, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, Center for Strategic Scientific Initiatives, National Cancer Institute, National Institutes of Health, 31 Center Drive, Bethesda, MD 20892, USA
| | | |
Collapse
|
25
|
Christie AE, Stemmler EA, Dickinson PS. Crustacean neuropeptides. Cell Mol Life Sci 2010; 67:4135-69. [PMID: 20725764 PMCID: PMC11115526 DOI: 10.1007/s00018-010-0482-8] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 07/09/2010] [Accepted: 07/28/2010] [Indexed: 10/19/2022]
Abstract
Crustaceans have long been used for peptide research. For example, the process of neurosecretion was first formally demonstrated in the crustacean X-organ-sinus gland system, and the first fully characterized invertebrate neuropeptide was from a shrimp. Moreover, the crustacean stomatogastric and cardiac nervous systems have long served as models for understanding the general principles governing neural circuit functioning, including modulation by peptides. Here, we review the basic biology of crustacean neuropeptides, discuss methodologies currently driving their discovery, provide an overview of the known families, and summarize recent data on their control of physiology and behavior.
Collapse
Affiliation(s)
- Andrew E Christie
- Program in Neuroscience, John W. and Jean C. Boylan Center for Cellular and Molecular Physiology, Mount Desert Island Biological Laboratory, Old Bar Harbor Road, P.O. Box 35, Salisbury Cove, ME 04672, USA.
| | | | | |
Collapse
|
26
|
Yu T, Peng H. Quantification and deconvolution of asymmetric LC-MS peaks using the bi-Gaussian mixture model and statistical model selection. BMC Bioinformatics 2010; 11:559. [PMID: 21073736 PMCID: PMC2993707 DOI: 10.1186/1471-2105-11-559] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 11/12/2010] [Indexed: 11/18/2022] Open
Abstract
Background Liquid chromatography-mass spectrometry (LC-MS) is one of the major techniques for the quantification of metabolites in complex biological samples. Peak modeling is one of the key components in LC-MS data pre-processing. Results To quantify asymmetric peaks with high noise level, we developed an estimation procedure using the bi-Gaussian function. In addition, to accurately quantify partially overlapping peaks, we developed a deconvolution method using the bi-Gaussian mixture model combined with statistical model selection. Conclusions Using extensive simulations and real data, we demonstrated the advantage of the bi-Gaussian mixture model over the Gaussian mixture model and the method of kernel smoothing combined with signal summation in peak quantification and deconvolution. The method is implemented in the R package apLCMS: http://www.sph.emory.edu/apLCMS/.
Collapse
Affiliation(s)
- Tianwei Yu
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
| | | |
Collapse
|
27
|
Krug K, Nahnsen S, Macek B. Mass spectrometry at the interface of proteomics and genomics. MOLECULAR BIOSYSTEMS 2010; 7:284-91. [PMID: 20967315 DOI: 10.1039/c0mb00168f] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
With the onset of modern DNA sequencing technologies, genomics is experiencing a revolution in terms of quantity and quality of sequencing data. Rapidly growing numbers of sequenced genomes and metagenomes present a tremendous challenge for bioinformatics tools that predict protein-coding regions. Experimental evidence of expressed genomic regions, both at the RNA and protein level, is becoming invaluable for genome annotation and training of gene prediction algorithms. Evidence of gene expression at the protein level using mass spectrometry-based proteomics is increasingly used in refinement of raw genome sequencing data. In a typical "proteogenomics" experiment, the whole proteome of an organism is extracted, digested into peptides and measured by a mass spectrometer. The peptide fragmentation spectra are identified by searching against a six-frame translation of the raw genomic assembly, thus enabling the identification of hitherto unpredicted protein-coding genomic regions. Application of mass spectrometry to genome annotation presents a range of challenges to the standard workflows in proteomics, especially in terms of proteome coverage and database search strategies. Here we provide an overview of the field and argue that the latest mass spectrometry technologies that enable high mass accuracy at high acquisition rates will prove to be especially well suited for proteogenomics applications.
Collapse
Affiliation(s)
- Karsten Krug
- Proteome Center Tuebingen, Interdepartmental Institute for Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tuebingen, Germany
| | | | | |
Collapse
|
28
|
Abramsson A, Westman-Brinkmalm A, Pannee J, Gustavsson M, von Otter M, Blennow K, Brinkmalm G, Kettunen P, Zetterberg H. Proteomics profiling of single organs from individual adult zebrafish. Zebrafish 2010; 7:161-8. [PMID: 20392139 DOI: 10.1089/zeb.2009.0644] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The model organism zebrafish (Danio rerio) is extensively utilized in studies of developmental biology but is also being investigated in the context of a growing list of human age-related diseases. To facilitate such studies, we here present protein expression patterns of adult zebrafish organs, including blood, brain, fin, heart, intestine, liver, and skeletal muscle. Protein extracts were prepared from the different organs of two zebrafish and analyzed using liquid chromatography coupled to high-resolution tandem mass spectrometry. Zebrafish tissue was digested directly after minimal fractionation and cleaned up (the shotgun approach). Proteins were identified using Mascot software. In total, 1394 proteins were identified of which 644 were nonredundant. Of these, 373 demonstrated an organ-specific expression pattern and 57 had not been shown on protein level before. These data emphasize the need for increased research at the protein level to facilitate the selection of candidate proteins for targeted quantification and to refine systematic genetic network analysis in vertebrate development, biology, and disease.
Collapse
Affiliation(s)
- Alexandra Abramsson
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
| | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Zmatliková Z, Sedláková P, Lacinová K, Eckhardt A, Pataridis S, Mikšík I. Non-enzymatic posttranslational modifications of bovine serum albumin by oxo-compounds investigated by high-performance liquid chromatography-mass spectrometry and capillary zone electrophoresis-mass spectrometry. J Chromatogr A 2010; 1217:8009-15. [PMID: 20828700 DOI: 10.1016/j.chroma.2010.08.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 08/04/2010] [Accepted: 08/06/2010] [Indexed: 02/05/2023]
Abstract
Non-enzymatic posttranslational modifications of bovine serum albumin (BSA) by various oxo-compounds (glucose, ribose, glyoxal and glutardialdehyde) have been investigated using high-performance liquid chromatography (HPLC) and capillary zone electrophoresis (CZE). Both of these methods used mass spectrometric (MS) detection. Three enzymes (trypsin, pepsin, proteinase K) were used to digest glycated BSA. The extent of modification depended on the selected oxo-compound. Reactivity increased progressively from glucose to glutardialdehyde (glucose<ribose<glyoxal<glutardialdehyde). Carboxymethylation of lysine (CML) was the main type of modification detected. The HPLC/MS method achieved higher coverage and a larger amount of CML was identified compared to CZE/MS.
Collapse
Affiliation(s)
- Zdeňka Zmatliková
- Institute of Physiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | | | | | | | | | | |
Collapse
|
30
|
Piñeiro C, Cañas B, Carrera M. The role of proteomics in the study of the influence of climate change on seafood products. Food Res Int 2010. [DOI: 10.1016/j.foodres.2009.11.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
31
|
|
32
|
Tumani H, Lehmensiek V, Lehnert S, Otto M, Brettschneider J. 2D DIGE of the cerebrospinal fluid proteome in neurological diseases. Expert Rev Proteomics 2010; 7:29-38. [PMID: 20121474 DOI: 10.1586/epr.09.99] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
2D DIGE is a promising approach to comparative proteome analysis known for a high sensitivity and high reproducibility compared with classical 2DE techniques. It offers new possibilities for the detection of cerebrospinal fluid (CSF) biomarkers in neurological diseases, such as dementia, amyotrophic lateral sclerosis or multiple sclerosis. We review the first studies using 2D DIGE for analysis of the CSF proteome in neurological diseases and discuss advantages, as well as drawbacks, of the methodological approach with special emphasis on CSF-related aspects.
Collapse
Affiliation(s)
- Hayrettin Tumani
- Department of Neurology, University of Ulm, Oberer Eselsberg 45, 89081 Ulm, Germany.
| | | | | | | | | |
Collapse
|
33
|
Hodgkinson VC, Eagle GL, Drew PJ, Lind MJ, Cawkwell L. Biomarkers of chemotherapy resistance in breast cancer identified by proteomics: current status. Cancer Lett 2010; 294:13-24. [PMID: 20176436 DOI: 10.1016/j.canlet.2010.01.036] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Revised: 01/26/2010] [Accepted: 01/29/2010] [Indexed: 11/26/2022]
Abstract
This review describes and discusses the advantages and limitations of proteomic approaches in the identification of biomarkers associated with chemotherapy resistance. Both gel-based (two-dimensional polyacrylamide gel electrophoresis) and gel-free (shotgun and quantitative) mass spectrometry approaches are discussed. Non-mass spectrometry approaches including antibody microarray platforms are described as complementary proteomic strategies. Methods for technical confirmation and clinical validation of putative biomarkers are presented. Use of this proteomic toolbox in the quest for biomarkers of chemotherapy resistance in breast cancer is reviewed. Technical aspects of sample selection, acquisition, storage and analysis are discussed and putative biomarkers identified through proteomic approaches are presented.
Collapse
Affiliation(s)
- Victoria C Hodgkinson
- Cancer Biology Proteomics Group, Postgraduate Medical Institute of the University of Hull, Hull, UK
| | | | | | | | | |
Collapse
|
34
|
Herzog G, Roger A, Sheehan D, Arrigan DWM. Ion-Transfer Voltammetric Behavior of Protein Digests at Liquid|Liquid Interfaces. Anal Chem 2009; 82:258-64. [DOI: 10.1021/ac901909j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Grégoire Herzog
- Tyndall National Institute, Lee Maltings, and Department of Biochemistry, University College Cork, Cork, Ireland
| | - Amandine Roger
- Tyndall National Institute, Lee Maltings, and Department of Biochemistry, University College Cork, Cork, Ireland
| | - David Sheehan
- Tyndall National Institute, Lee Maltings, and Department of Biochemistry, University College Cork, Cork, Ireland
| | - Damien W. M. Arrigan
- Tyndall National Institute, Lee Maltings, and Department of Biochemistry, University College Cork, Cork, Ireland
| |
Collapse
|
35
|
Ahmed FE. The role of capillary electrophoresis–mass spectrometry to proteome analysis and biomarker discovery. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:1963-81. [DOI: 10.1016/j.jchromb.2009.05.023] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2008] [Revised: 04/24/2009] [Accepted: 05/10/2009] [Indexed: 01/25/2023]
|
36
|
Ahmed FE. Liquid chromatography–mass spectrometry: a tool for proteome analysis and biomarker discovery and validation. ACTA ACUST UNITED AC 2009; 3:429-44. [DOI: 10.1517/17530050902832855] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
37
|
Ahmed FE. Sample preparation and fractionation for proteome analysis and cancer biomarker discovery by mass spectrometry. J Sep Sci 2009; 32:771-98. [PMID: 19219839 DOI: 10.1002/jssc.200800622] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Sample preparation and fractionation technologies are one of the most crucial processes in proteomic analysis and biomarker discovery in solubilized samples. Chromatographic or electrophoretic proteomic technologies are also available for separation of cellular protein components. There are, however, considerable limitations in currently available proteomic technologies as none of them allows for the analysis of the entire proteome in a simple step because of the large number of peptides, and because of the wide concentration dynamic range of the proteome in clinical blood samples. The results of any undertaken experiment depend on the condition of the starting material. Therefore, proper experimental design and pertinent sample preparation is essential to obtain meaningful results, particularly in comparative clinical proteomics in which one is looking for minor differences between experimental (diseased) and control (nondiseased) samples. This review discusses problems associated with general and specialized strategies of sample preparation and fractionation, dealing with samples that are solution or suspension, in a frozen tissue state, or formalin-preserved tissue archival samples, and illustrates how sample processing might influence detection with mass spectrometric techniques. Strategies that dramatically improve the potential for cancer biomarker discovery in minimally invasive, blood-collected human samples are also presented.
Collapse
Affiliation(s)
- Farid E Ahmed
- Department of Radiation Oncology, Leo W. Jenkins Cancer Center, The Brody School of Medicine at East Carolina University, Greenville, NC, USA.
| |
Collapse
|