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Inter-Alpha-Trypsin Inhibitor Heavy Chain 4 Plays an Important Role in the Development and Reproduction of Nilaparvata lugens. INSECTS 2022; 13:insects13030303. [PMID: 35323600 PMCID: PMC8951764 DOI: 10.3390/insects13030303] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/07/2022] [Accepted: 03/15/2022] [Indexed: 12/18/2022]
Abstract
Simple Summary The brown planthopper, Nilaparvata lugens (Hemiptera: Delphacidae), is a destructive insect pest of rice. It causes reductions in rice yield and great economic losses. In this study, we used RNAi to explore the function of the inter-alpha-trypsin inhibitor heavy chain 4 (ITIH4) gene in the development and reproduction of the brown planthopper. Our results revealed that ITIH4 influences the survival, ovarian development, egg production, and egg hatching of this insect, indicating that ITIH4 plays important roles in development and reproduction. Considering the importance of ITIH4 in the brown planthopper, it may be a potential target for pest management. Abstract The brown planthopper, Nilaparvata lugens, is a difficult-to-control insect pest affecting rice yields in Asia. As a structural component of the inter-alpha-trypsin inhibitor (ITI), the inter-alpha-trypsin inhibitor heavy chain (ITIH) has been reported to be involved in various inflammatory or malignant disorders, ovarian development, and ovulation. To reveal the function of ITIH4 in N. lugens, the gene encoding N. lugens ITIH4 (NlITIH4) was cloned and characterized. NlITIH4 contains a signal peptide, a vault protein inter-alpha-trypsin domain, and a von Willebrand factor type A domain. qPCR analysis showed that NlITIH4 was expressed at all developmental stages and in all tissues (fat body, ovary, and gut), with the highest expression in the fat body. Double stranded NlITIH4 (dsNlITIH4) injection clearly led to an RNAi-mediated inhibition of the expression of NlITIH4 and resulted in reduced survival, delayed ovarian development, and reduced egg production and egg hatching. These results indicate that NlITIH4 plays an important role in the development and reproduction of N. lugens.
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2
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Dunphy K, O’Mahoney K, Dowling P, O’Gorman P, Bazou D. Clinical Proteomics of Biofluids in Haematological Malignancies. Int J Mol Sci 2021; 22:ijms22158021. [PMID: 34360786 PMCID: PMC8348619 DOI: 10.3390/ijms22158021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/23/2021] [Accepted: 07/23/2021] [Indexed: 12/25/2022] Open
Abstract
Since the emergence of high-throughput proteomic techniques and advances in clinical technologies, there has been a steady rise in the number of cancer-associated diagnostic, prognostic, and predictive biomarkers being identified and translated into clinical use. The characterisation of biofluids has become a core objective for many proteomic researchers in order to detect disease-associated protein biomarkers in a minimally invasive manner. The proteomes of biofluids, including serum, saliva, cerebrospinal fluid, and urine, are highly dynamic with protein abundance fluctuating depending on the physiological and/or pathophysiological context. Improvements in mass-spectrometric technologies have facilitated the in-depth characterisation of biofluid proteomes which are now considered hosts of a wide array of clinically relevant biomarkers. Promising efforts are being made in the field of biomarker diagnostics for haematologic malignancies. Several serum and urine-based biomarkers such as free light chains, β-microglobulin, and lactate dehydrogenase are quantified as part of the clinical assessment of haematological malignancies. However, novel, minimally invasive proteomic markers are required to aid diagnosis and prognosis and to monitor therapeutic response and minimal residual disease. This review focuses on biofluids as a promising source of proteomic biomarkers in haematologic malignancies and a key component of future diagnostic, prognostic, and disease-monitoring applications.
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Affiliation(s)
- Katie Dunphy
- Department of Biology, National University of Ireland, W23 F2K8 Maynooth, Ireland; (K.D.); (P.D.)
| | - Kelly O’Mahoney
- Department of Haematology, Mater Misericordiae University Hospital, D07 WKW8 Dublin, Ireland; (K.O.); (P.O.)
| | - Paul Dowling
- Department of Biology, National University of Ireland, W23 F2K8 Maynooth, Ireland; (K.D.); (P.D.)
| | - Peter O’Gorman
- Department of Haematology, Mater Misericordiae University Hospital, D07 WKW8 Dublin, Ireland; (K.O.); (P.O.)
| | - Despina Bazou
- Department of Haematology, Mater Misericordiae University Hospital, D07 WKW8 Dublin, Ireland; (K.O.); (P.O.)
- Correspondence:
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3
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Soler L, Szczubiał M, Dąbrowski R, Płusa A, Bochniarz M, Brodzki P, Lampreave F, Piñeiro M. Measurement of ITIH4 and Hp levels in bitches with pyometra using newly developed ELISA methods. Vet Immunol Immunopathol 2021; 235:110221. [PMID: 33730638 DOI: 10.1016/j.vetimm.2021.110221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 02/22/2021] [Accepted: 02/27/2021] [Indexed: 12/01/2022]
Abstract
Measurement of acute phase proteins (APPs) as biomarkers in canine medicine is in increasing demand. In the present study, the development and validation of two ELISA methods for the quantification of canine inter-alpha-trypsin inhibitor heavy chain 4 (ITIH4) and haptoglobin (Hp) are shown. The adequate imprecision and accuracy and wide analytical range make the developed methods appropriate to quantify ITIH4 and Hp in serum samples. The inter- and intra-assay CVs were lower than 10 %, and the assays maintained linearity under dilution and showed analytical equivalence with the method of radial immunodiffusion. The measurement of CRP, Hp and ITIH4 in sera from bitches affected by pyometra allowed us to determine that ITIH4 behaves as a moderate APP in dogs. The group of bitches affected by pyometra showed very high levels of CRP (147 ± 91 mg/L), corresponding to a strong inflammatory process, which resulted in a moderate increase in the concentrations of Hp (7 times) and ITIH4 (3 times) compared to the control group.
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Affiliation(s)
- Lourdes Soler
- Acuvet Biotech, C/Bari 25 dpdo, Zaragoza, 50197, Spain.
| | - Marek Szczubiał
- Department and Clinic of Animal Reproduction, Faculty of Veterinary Medicine, University of Life Sciences, Gleboka 30, Lublin, 20-612, Poland
| | - Roman Dąbrowski
- Department and Clinic of Animal Reproduction, Faculty of Veterinary Medicine, University of Life Sciences, Gleboka 30, Lublin, 20-612, Poland
| | - Anna Płusa
- Department and Clinic of Animal Reproduction, Faculty of Veterinary Medicine, University of Life Sciences, Gleboka 30, Lublin, 20-612, Poland
| | - Mariola Bochniarz
- Department and Clinic of Animal Reproduction, Faculty of Veterinary Medicine, University of Life Sciences, Gleboka 30, Lublin, 20-612, Poland
| | - Piotr Brodzki
- Department and Clinic of Animal Reproduction, Faculty of Veterinary Medicine, University of Life Sciences, Gleboka 30, Lublin, 20-612, Poland
| | - Fermín Lampreave
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, Zaragoza, 50009, Spain
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4
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Liu D, Liu G, Li Y, Wang Y, Zheng Y, Sha S, Li W, Kameyama A, Dong W. Rapid glycosylation analysis of mouse serum glycoproteins separated by supported molecular matrix electrophoresis. J Proteomics 2021; 234:104098. [PMID: 33421637 DOI: 10.1016/j.jprot.2020.104098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 12/06/2020] [Accepted: 12/29/2020] [Indexed: 11/30/2022]
Abstract
Previously, we developed a novel separation technique, namely, supported molecular matrix electrophoresis (SMME), which separates mucins on a PVDF membrane that impregnated with a hydrophilic polymer (such as polyvinyl alcohol), so it has the characteristics that are compatible with glycan analysis of the separated bands. Here, we describe the first instance of the application of SMME to mouse sera fractionation and demonstrate their differences from the pooled human sera fractionation by SMME. Furthermore, we have developed a fixation method for the lectin blotting of SMME-separated glycoproteins by immersing the SMME membranes into acetone solvent followed by heating. It showed that the amount of protein samples required for SMME were reduced more than 4-fold than that of the process of SDS-PAGE. We applied these techniques for the detection of glycosylation patterns of serum proteins from Fut8+/+ and Fut8-/- mice, further analyzed N-linked and O-linked glycans from the separated γ-bands by mass spectrometry, and demonstrated that there are α2,8-sialylated O-glycans contained in mouse sera glycoproteins. SMME can provide simple, rapid sera fractionation, glycan profiling differences between the bands of two samples and a new insight into the underlying mechanism that responsible for related diseases. SIGNIFICANCE: We describe that the first application of SMME can separate mouse serum proteins into six bands and identify the major protein components of each fraction in mouse serum separated by SMME. Furthermore, we successfully developed a fixation method for lectin blotting of SMME-separated glycoproteins and applied to the detection of glycosylation patterns of serum glycoproteins from Fut8+/+ and Fut8-/- mice, also, the method is promising for detecting glycan profiling differences between two samples in both research and clinical settings.
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Affiliation(s)
- Dongqi Liu
- China Medical University - The Queen's University of Belfast Joint College, Shenyang 110122, Liaoning, China
| | - Gang Liu
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, Liaoning, China
| | - Yuqing Li
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, Liaoning, China
| | - Yue Wang
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, Liaoning, China
| | - Yuanyuan Zheng
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, Liaoning, China
| | - Shanshan Sha
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, Liaoning, China
| | - Wenzhe Li
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, Liaoning, China
| | - Akihiko Kameyama
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Open Space Laboratory C-2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Weijie Dong
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, Liaoning, China.
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Teclemariam ET, Pergande MR, Cologna SM. Considerations for mass spectrometry-based multi-omic analysis of clinical samples. Expert Rev Proteomics 2020; 17:99-107. [PMID: 31996049 DOI: 10.1080/14789450.2020.1724540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Introduction: The role of mass spectrometry in biomolecule analysis has become paramount over the last several decades ranging in the analysis across model systems and human specimens. Accordingly, the presence of mass spectrometers in clinical laboratories has also expanded alongside the number of researchers investigating the protein, lipid, and metabolite composition of an array of biospecimens. With this increase in the number of omic investigations, it is important to consider the entire experimental strategy from sample collection and storage, data collection and analysis.Areas covered: In this short review, we outline considerations for working with clinical (e.g. human) specimens including blood, urine, and cerebrospinal fluid, with emphasis on sample handling, profiling composition, targeted measurements and relevance to disease. Discussions of integrated genomic or transcriptomic datasets are not included. A brief commentary is also provided regarding new technologies with clinical relevance.Expert opinion: The role of mass spectrometry to investigate clinically related specimens is on the rise and the ability to integrate multiple omics datasets from mass spectrometry measurements will be crucial to further understanding human health and disease.
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Affiliation(s)
- Esei T Teclemariam
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Melissa R Pergande
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Stephanie M Cologna
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA.,Laboratory of Integrated Neuroscience, University of Illinois at Chicago, Chicago, IL, USA
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6
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Soler L, García N, Andrés M, Armengol R, Lampreave F, Alava MA, Piñeiro M. Development and validation of an ELISA for the quantification of bovine ITIH4 in serum and milk. Vet Immunol Immunopathol 2019; 217:109922. [PMID: 31450165 DOI: 10.1016/j.vetimm.2019.109922] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 07/31/2019] [Accepted: 08/07/2019] [Indexed: 12/12/2022]
Abstract
Inter alpha trypsin inhibitor heavy chain 4 (ITIH4) is a serum protein belonging to the Inter alpha trypsin inhibitor (ITI) family, which was previously characterized by our group as a new APP in cattle. This protein was firstly described in pigs where is known to be a major acute phase protein, also denominated Pig-MAP. Increases of ITIH4 of up to 12 times the pre-infection values were previously reported in the serum of heifers with experimentally induced summer mastitis. ITIH4 was detected in the milk of cows with mastitis by western blot, but the method previously used to quantify this protein, radial immunodiffusion, was not sensitive enough to quantify it in milk samples. In this study we developed an ELISA method which allows the quantification of bovine ITIH4 in serum and milk samples. Previously developed antibodies were used to perform the assay, including anti bovine ITIH4 polyclonal antibodies and a monoclonal antibody against pig ITIH4 that also recognizes the bovine homologous protein. The ELISA developed showed an adequate precision, with inter and intra- assay coefficients of variation lower than 10% for serum and milk samples. The assay keeps linearity under dilution for both serum and milk samples. A good agreement was observed between the values measured by ELISA and radial immunodiffusion in serum samples.
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Affiliation(s)
- Lourdes Soler
- Acuvet Biotech, C/ Bari 25 dpdo, 50197, Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Natalia García
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Marta Andrés
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Ramón Armengol
- Departament de Ciència Animal, ETSEA, University of Lleida, Av. Alcalde Rovira Roure 191, E25198, Lleida, Spain
| | - Fermín Lampreave
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - María A Alava
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain
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7
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Lynch KB, Ren J, Beckner MA, He C, Liu S. Monolith columns for liquid chromatographic separations of intact proteins: A review of recent advances and applications. Anal Chim Acta 2018; 1046:48-68. [PMID: 30482303 DOI: 10.1016/j.aca.2018.09.021] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/10/2018] [Accepted: 09/11/2018] [Indexed: 01/20/2023]
Abstract
In this article we survey 256 references (with an emphasis on the papers published in the past decade) on monolithic columns for intact protein separation. Protein enrichment and purification are included in the broadly defined separation. After a brief introduction, we describe the types of monolithic columns and modes of chromatographic separations employed for protein separations. While the majority of the work is still in the research and development phase, papers have been published toward utilizing monolithic columns for practical applications. We survey these papers as well in this review. Characteristics of selected methods along with their pros and cons will also be discussed.
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Affiliation(s)
- Kyle B Lynch
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, United States
| | - Jiangtao Ren
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, United States
| | - Matthew A Beckner
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, United States
| | - Chiyang He
- School of Chemistry and Chemical Engineering, Wuhan Textile University, 1 Textile Road, Wuhan, 430073, PR China
| | - Shaorong Liu
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, United States.
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8
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Boschetti E, D'Amato A, Candiano G, Righetti PG. Protein biomarkers for early detection of diseases: The decisive contribution of combinatorial peptide ligand libraries. J Proteomics 2017; 188:1-14. [PMID: 28882677 DOI: 10.1016/j.jprot.2017.08.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 08/09/2017] [Accepted: 08/13/2017] [Indexed: 12/31/2022]
Abstract
The present review deals with biomarker discovery, especially in regard to sample treatment via combinatorial peptide ligand libraries, perhaps the only technique at present allowing deep exploration of biological fluids and tissue extracts in search for low- to very-low-abundance proteins, which could possibly mark the onset of most pathologies. Early-stage biomarkers, in fact, might be the only way to detect the beginning of most diseases thus permitting proper intervention and care. The following cancers are reviewed, with lists of potential biomarkers suggested in various reports: hepatocellular carcinoma, ovarian cancer, breast cancer and pancreatic cancer, together with some other interesting applications. Although panels of proteins have been presented, with robust evidence, as potential early-stage biomarkers in these different pathologies, their approval by FDA as novel biomarkers in routine clinical chemistry settings would require plenty of additional work and efforts from the pharma industry. The science environment in universities could simply not afford such heavy monetary investments. SIGNIFICANCE After more than 16years of search for novel biomarkers, to be used in a clinical chemistry set-up, via proteomic analysis (mostly in biological fluids) it was felt a critical review was due. In the present report, though, only papers reporting biomarker discovery via combinatorial peptide ligand libraries are listed and assessed, since this methodology seems to be the most advanced one for digging in depth into low-to very-low-abundance proteins, which might represent important biomarkers for the onset of pathologies. In particular, a large survey has been made for the following diseases, since they appear to have a large incidence on human population and/or represent fatal diseases: ovarian cancer, breast cancer, pancreatic cancer and hepatocellular carcinoma.
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Affiliation(s)
| | - Alfonsina D'Amato
- Quadram Institute of Bioscience, Norwich Research Park, NR4 7UA Norwich, UK
| | - Giovanni Candiano
- Nephrology, Dialysis, Transplantation Unit and Laboratory on Pathophysiology of Uremia, Istituto Giannina Gaslini, Genoa, Italy
| | - Pier Giorgio Righetti
- Politecnico di Milano, Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Via Mancinelli 7, Milano 20131, Italy.
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9
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Identification of potential serum biomarkers in pigs at early stage after Lipopolysaccharide injection. Res Vet Sci 2017; 111:140-146. [PMID: 28249176 DOI: 10.1016/j.rvsc.2017.02.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 01/03/2017] [Accepted: 02/02/2017] [Indexed: 11/23/2022]
Abstract
The identification of useful biological indicators to monitor the body response before the presentation of clinical diseases has practical value in livestock production. To identify potential biomarkers in pigs at the early stage during inflammation, 12 pigs were intramuscularly injected with 2mL of Lipopolysaccharide (LPS, 15μg/kg BW) or saline. Serum protein expression profiles were detected with two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) techniques. Serum biochemical indicators and acute phase protein (APP) concentrations were analyzed with an automatic biochemical analyzer and ELISA, respectively. Of the serum biochemical indicators, creatinine concentration significantly increased 6h post infection, whereas albumin showed a decreased tendency. The 2-DE and MALDI-TOF mass spectrometry technique detected 17 protein spots representing 10 proteins: α-1-antichymotrypsin, albumin, bovine lactoferrin, serotransferrin, serpin A3-6, immunoglobulin light chain (κ chain, mu chain), complement C3 precursor, zinc-α-2-glycoprotein (ZAG), and ceruloplasmin. Two proteins were selected to confirm the mass spectrometry results, and resulting differences accorded with the proteomics results. Of the four typical acute phase protein (APPs) measured, the C-reactive protein (CRP) and haptoglobin (HP) concentrations increased significantly, while no differences were observed in the pig-major acute phase protein (Pig-MAP) and transthyretin (TTR) contents. The results showed that serum creatinine, CRP, HP, and ten other proteins content changed significantly after LPS injection. Of these proteins, ZAG was first reported in pigs during inflammation. These proteins show great promise as biomarkers to monitor the health status and welfare of pigs during the early stage of LPS-induced inflammation.
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10
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Soler L, García N, Unzueta A, Piñeiro M, Álava M, Lampreave F. Purification and determination of C-reactive protein and inter-α-trypsin inhibitor heavy chain 4 in dogs after major surgery through generation of specific antibodies. Vet Immunol Immunopathol 2016; 179:26-31. [DOI: 10.1016/j.vetimm.2016.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/12/2016] [Accepted: 07/20/2016] [Indexed: 12/12/2022]
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Wan-Ibrahim WI, Singh VA, Hashim OH, Abdul-Rahman PS. Biomarkers for Bone Tumors: Discovery from Genomics and Proteomics Studies and Their Challenges. Mol Med 2015; 21:861-872. [PMID: 26581086 DOI: 10.2119/molmed.2015.00183] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 11/12/2015] [Indexed: 01/07/2023] Open
Abstract
Diagnosis of bone tumor currently relies on imaging and biopsy, and hence, the need to find less invasive ways for its accurate detection. More recently, numerous promising deoxyribonucleic acid (DNA) and protein biomarkers with significant prognostic, diagnostic and/or predictive abilities for various types of bone tumors have been identified from genomics and proteomics studies. This article reviewed the putative biomarkers for the more common types of bone tumors (that is, osteosarcoma, Ewing sarcoma, chondrosarcoma [malignant] and giant cell tumor [benign]) that were unveiled from the studies. The benefits and drawbacks of these biomarkers, as well as the technology platforms involved in the research, were also discussed. Challenges faced in the biomarker discovery studies and the problems in their translation from the bench to the clinical settings were also addressed.
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Affiliation(s)
- Wan I Wan-Ibrahim
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Vivek A Singh
- Department of Orthopaedic Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Onn H Hashim
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.,University of Malaya Centre of Proteomics Research (UMCPR), University of Malaya, Kuala Lumpur, Malaysia
| | - Puteri S Abdul-Rahman
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.,University of Malaya Centre of Proteomics Research (UMCPR), University of Malaya, Kuala Lumpur, Malaysia
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12
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Muckova P, Wendler S, Rubel D, Büchler R, Alert M, Gross O, Rhode H. Preclinical Alterations in the Serum of COL(IV)A3–/– Mice as Early Biomarkers of Alport Syndrome. J Proteome Res 2015; 14:5202-14. [DOI: 10.1021/acs.jproteome.5b00814] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Petra Muckova
- Institute
of Biochemistry I, University Hospital Jena, Nonnenplan 2-4, 07740 Jena, Germany
- Clinic
of Neurology, University Hospital Jena, Erlanger Allee 101, 07740 Jena, Germany
| | - Sindy Wendler
- Institute
of Biochemistry I, University Hospital Jena, Nonnenplan 2-4, 07740 Jena, Germany
| | - Diana Rubel
- Department
of Nephrology and Rheumatology, University Medicine Göttingen, Robert-Koch Str. 40, 37075 Göttingen, Germany
| | - Rita Büchler
- Institute
of Biochemistry I, University Hospital Jena, Nonnenplan 2-4, 07740 Jena, Germany
| | - Mandy Alert
- Institute
of Biochemistry I, University Hospital Jena, Nonnenplan 2-4, 07740 Jena, Germany
| | - Oliver Gross
- Department
of Nephrology and Rheumatology, University Medicine Göttingen, Robert-Koch Str. 40, 37075 Göttingen, Germany
| | - Heidrun Rhode
- Institute
of Biochemistry I, University Hospital Jena, Nonnenplan 2-4, 07740 Jena, Germany
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Abstract
Understanding changes in the expression of specific proteins and/or alterations in their posttranslational modifications is crucial to elucidating the molecular mechanisms underlying disease states such as alcoholic liver disease. Protein separation and analysis techniques such as two-dimensional electrophoresis and mass spectrometry can be used for identifying biomarker proteins that are altered during progression of alcoholic liver disease. In this chapter, we outline methods for resolving liver tissue proteins from a rodent model of alcoholic liver disease using two-dimensional electrophoresis and identifying differentially expressed proteins using mass spectrometry. In addition, since oxidative stress strongly correlates with alcoholic liver disease, we also describe methods for identifying oxidatively modified proteins from liver tissue. We specifically focus on identifying proteins that are carbonylated as protein carbonylation is a permanent modification and considered deleterious to cells. The combination of two-dimensional electrophoresis for protein resolution, mass spectrometry for protein identification, and affinity-based methods for enriching and identifying carbonylated proteins is a powerful methodology for protein biomarker identification.
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14
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Wang F, Huang L, Na N, He D, Sun D, Ouyang J. The development of simple and sensitive small-molecule fluorescent probes for the detection of serum proteins after native polyacrylamide gel electrophoresis. Analyst 2012; 137:2367-73. [PMID: 22475746 DOI: 10.1039/c2an35265f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, a simple and sensitive small-molecule fluorescent probe, 2,5-dihydroxy-4'-dimethylaminochalcone (DHDMAC), was designed and synthesized for the detection of human serum proteins via hydrophobic interactions after polyacrylamide gel electrophoresis (PAGE). This probe produced lower fluorescence emission in the absence of proteins, and the emission intensity was significantly increased after the interaction with serum proteins. To demonstrate the imaging performance of this probe as a fluorescent dye, a series of experiments was conducted that included sensitivity comparison and 2D-PAGE. The results indicated that the sensitivity of DHDMAC staining is comparable to that of the most widely used fluorescent dye, SYPRO Ruby, and more protein spots (including thyroxine-binding globulin, angiotensinogen, afamin, zinc-α-2-glycoprotein and α-1-antichymotrypsin) were detected after 2D-PAGE. Therefore, DHDMAC is a good protein reporter due to its fast staining procedure, low detection limits and high resolution.
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Affiliation(s)
- Fangfang Wang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
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15
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Gianazza E, Vegeto E, Eberini I, Sensi C, Miller I. Neglected markers: Altered serum proteome in murine models of disease. Proteomics 2012; 12:691-707. [DOI: 10.1002/pmic.201100320] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 08/28/2011] [Indexed: 11/09/2022]
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Alonso-Fauste I, Andrés M, Iturralde M, Lampreave F, Gallart J, Alava MA. Proteomic characterization by 2-DE in bovine serum and whey from healthy and mastitis affected farm animals. J Proteomics 2011; 75:3015-30. [PMID: 22193514 DOI: 10.1016/j.jprot.2011.11.035] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 11/25/2011] [Accepted: 11/29/2011] [Indexed: 10/14/2022]
Abstract
Acute phase proteins (APP) have been identified in whey and sera from healthy and mastitis cows through the proteomic analysis using two-dimensional electrophoresis (2-DE) coupled with Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). Although normal and mastitis serum samples show relatively similar protein composition, marked differences in expression levels and patterns can be observed. Conversely, normal and mastitis whey showed a very different composition, likely due to extravasation of blood proteins to the mammary gland. Different isoforms from the most abundant protein in milk, casein, were detected in both normal and mastitis whey. Other proteins, such as lactotransferrin, were only detected in the inflamed animal samples. Immunoglobulins showed different patterns but not increased levels in the inflamed whey. Also, many cellular proteins in mastitis cow's whey, that were absent from healthy cow's milk. They are responsible for the great change in composition between normal and mastitis whey, especially those which exert a biological function related to immune defense. Data collected in this work are of interest for gaining information about physiological changes in protein patterns in different fluids and, the correspondent modifications as result of an acute phase process in farm. This article is part of a Special Issue entitled: Proteomics: The clinical link.
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Affiliation(s)
- Idoia Alonso-Fauste
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna, 12, 50009-Zaragoza, Spain
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17
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Zhu P, Bowden P, Zhang D, Marshall JG. Mass spectrometry of peptides and proteins from human blood. MASS SPECTROMETRY REVIEWS 2011; 30:685-732. [PMID: 24737629 DOI: 10.1002/mas.20291] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 12/09/2009] [Accepted: 01/19/2010] [Indexed: 06/03/2023]
Abstract
It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.
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Affiliation(s)
- Peihong Zhu
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario, Canada M5B 2K3
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18
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Sun B, Huang L, Na N, He D, Ouyang J. Applications of multifunctional magnetic nanoparticles for the enrichment of proteins for PAGE separation. Electrophoresis 2011; 32:2091-8. [DOI: 10.1002/elps.201000657] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Revised: 03/13/2011] [Accepted: 04/20/2011] [Indexed: 11/09/2022]
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19
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Sjölund M, Fossum C, Martín de la Fuente AJ, Alava M, Juul-Madsen HR, Lampreave F, Wallgren P. Effects of different antimicrobial treatments on serum acute phase responses and leucocyte counts in pigs after a primary and a secondary challenge infection with Actinobacillus pleuropneumoniae. Vet Rec 2011; 169:70. [PMID: 21737462 DOI: 10.1136/vr.d2268] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The susceptibility to an initial challenge and a re-challenge inoculation with Actinobacillus pleuropneumoniae was analysed in pigs that were treated with antimicrobials of different efficacies following the first exposure to A pleuropneumoniae. In brief, 30 nine-week-old specific pathogen-free pigs were allocated to five groups of six. After acclimatisation, four groups were inoculated with A pleuropneumoniae serotype 2. At the onset of clinical signs, three of the groups of pigs were treated with enrofloxacin, tetracycline or penicillin. A fourth group served as the inoculated control and the fifth group as a control group that had not been inoculated. On day 28, all five groups were re-challenged with the same strain of A pleuropneumoniae serotype 2 as had been used in the first inoculation. No treatments were carried out at this time. The acute phase responses and differential leucocyte counts were monitored in detail after both inoculations. Leucocytosis and acute phase responses in the forms of serum amyloid A, pig-major acute phase protein and haptoglobin were recorded in all of the inoculated groups after the onset of clinical signs following the first inoculation. A porcine mannan-binding lectin-A response was less evident in the pigs. Acute phase responses resembling those of the first inoculation were observed in the pigs that had not previously been inoculated and in the pigs treated with enrofloxacin. Acute phase responses were not recorded in the other three groups, where the pigs had seroconverted to A pleuropneumoniae serotype 2 following the first inoculation.
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Affiliation(s)
- M Sjölund
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute, 751 89 Uppsala, Sweden.
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20
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Dreisbach A, van der Kooi-Pol MM, Otto A, Gronau K, Bonarius HPJ, Westra H, Groen H, Becher D, Hecker M, van Dijl JM. Surface shaving as a versatile tool to profile global interactions between human serum proteins and the Staphylococcus aureus cell surface. Proteomics 2011; 11:2921-30. [PMID: 21674804 DOI: 10.1002/pmic.201100134] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2011] [Revised: 04/01/2011] [Accepted: 05/03/2011] [Indexed: 11/09/2022]
Abstract
The human commensal bacterium Staphylococcus aureus is renowned as a causative agent of severe invasive diseases. Upon entering the bloodstream, S. aureus can infect almost every tissue and organ system in the human body. To withstand insults from the immune system upon invasion, several immune-evasive mechanisms have evolved in S. aureus, such as complement inhibition by secreted proteins and IgG-binding by surface-exposed protein A. While it is generally accepted that S. aureus cells bind a range of host factors for various purposes, no global analyses to profile staphylococcal host factor binding have so far been performed. Therefore, we explored the possibility to profile the binding of human serum proteins to S. aureus cells by "surface shaving" with trypsin and subsequent MS analysis of liberated peptides. This resulted in the identification of several components of the complement system, the platelet factor 4 and the isoform 1 of the inter-α-trypsin inhibitor heavy chain H4 on the staphylococcal cell surface. We conclude that surface shaving is a versatile tool to profile global interactions between human serum proteins and the S. aureus cell surface.
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Affiliation(s)
- Annette Dreisbach
- Department of Medical Microbiology, University Medical Center Groningen and University of Groningen, Hanzeplein 1, Groningen, The Netherlands
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21
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Schwamborn K, Gaisa NT, Henkel C. Tissue and serum proteomic profiling for diagnostic and prognostic bladder cancer biomarkers. Expert Rev Proteomics 2011; 7:897-906. [PMID: 21142890 DOI: 10.1586/epr.10.82] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A panel of biomarkers for the early detection of bladder cancer has not yet been identified. Many different molecules, including DNA, RNA or proteins have been reported but none have provided adequate sensitivity for a single-tier screening test or a test to replace cystoscopy. Therefore, multimarker panels are discussed at present to give a more-precise answer to the biomarker quest. Mass spectrometry or 2D gel-electrophoresis have evolved greatly within recent years and are capable of analyzing multiple proteins or peptides in parallel with high sensitivity and specificity. However, transmission of screening results from one laboratory to another is still the main pitfall of those methods; a fact that emphasizes the need for consistent and standardized procedures as suggested by the Human Proteome Organization (HUPO). In this article, recent results in screening approaches and other proteomic techniques used for biomarker evaluation in bladder cancer are discussed with a focus on serum and tissue biomarkers.
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Affiliation(s)
- Kristina Schwamborn
- Institute of Pathology, RWTH Aachen University, Pauwelsstrasse 30, Aachen, Germany.
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22
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Spiller F, Costa C, Souto FO, Vinchi F, Mestriner FLAC, Laure HJ, Alves-Filho JC, Freitas A, Rosa JC, Ferreira SH, Altruda F, Hirsch E, Greene LJ, Tolosano E, Cunha FQ. Inhibition of neutrophil migration by hemopexin leads to increased mortality due to sepsis in mice. Am J Respir Crit Care Med 2010; 183:922-31. [PMID: 20971829 DOI: 10.1164/rccm.201002-0223oc] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE The reduction of neutrophil migration to the bacterial focus is associated with poor outcome in sepsis. OBJECTIVES The objective of this study was to identify soluble substances in the blood of septic mice that inhibit neutrophil migration. METHODS A pool of serum obtained from mice 2 hours after the induction of severe sepsis by cecal ligation and puncture inhibited the neutrophil migration. The proteins with inhibitory activity on neutrophil migration were isolated by Blue-Sepharose chromatography, high-performance liquid chromatography, and electrophoresis, and identified by mass spectrometry. MEASUREMENTS AND MAIN RESULTS Hemopexin was identified as the serum component responsible for the inhibition of neutrophil migration. In sepsis, the pretreatment of wild-type mice with hemopexin inhibited neutrophil migration to the focus of infection and decreased the survival rate from 87.5 to 50.0%. Hemopexin-null mice subjected to severe sepsis presented normal neutrophil migration, low bacteremia, and an improvement of 40% in survival rate. Moreover, hemopexin inhibited the neutrophil chemotaxis response evoked by C5a or macrophage inflammatory protein-2 and induced a reduction of CXCR2 and L-selectin as well as the up-regulation of CD11b expression in neutrophil membranes. The inhibitory effect of hemopexin on neutrophil chemotaxis was prevented by serine protease inhibitors or ATP. In addition, serum levels of ATP were decreased 2 hours after severe sepsis. CONCLUSIONS These data demonstrate for the first time the inhibitory role of hemopexin in neutrophil migration during sepsis and suggest that the therapeutic inhibition of hemopexin or its protease activity could improve neutrophil migration to the focus of infection and survival in sepsis.
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Affiliation(s)
- Fernando Spiller
- Department of Pharmacology, University of São Paulo, Av. Bandeirantes, Ribeirão Preto, SP, Brazil
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23
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Liu X, Huang L, Baeyens WRG, Ouyang J, He D, Wan G, Zhang L. Development of sensitive metalloporphyrin probes for chemiluminescent imaging detection of serum proteins. Electrophoresis 2009; 30:3034-3040. [PMID: 19711378 DOI: 10.1002/elps.200900151] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The development of metalloporphyrin- (ferric protoporphyrin IX chloride (FePP), cobalt (III) protoporphyrin IX chloride, copper (II) protoporphyrin IX) enhanced chemiluminescent (CL) imaging detection of serum proteins after PAGE is described in this article. The detection is based on the catalytic activity of metalloporphyrins, especially FePP, in the CL reaction of the luminol-H2O2 system. Some relatively low abundant proteins such as hemopexin (Hpx) and complement C4 are sensitively detected by FePP-enhanced CL imaging. Other proteins such as haptoglobin, apolipoprotein A-1, complement C3, and alpha-1-antitrypsin are also detected and identified by MS and MS/MS techniques. Detection limit of Hpx is as low as 20 ng, without the need of expensive antibodies or tedious immunoassay procedures. The mechanism of the proposed method is discussed employing standard proteins. The application to the analysis of different protein patterns in healthy people and in Thalassemia patients is being investigated.
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Affiliation(s)
- Xia Liu
- College of Chemistry, Beijing Normal University, Beijing, P. R. China
| | - Lingyun Huang
- Institute of Cell Biology, Beijing Normal University, Beijing, P. R. China
| | - Willy R G Baeyens
- Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Jin Ouyang
- College of Chemistry, Beijing Normal University, Beijing, P. R. China
| | - Dacheng He
- Institute of Cell Biology, Beijing Normal University, Beijing, P. R. China
| | - Genping Wan
- Department of Hematology, Guangzhou Children's Hospital, Guangzhou, P. R. China
| | - Li Zhang
- Department of Hematology, Guangzhou Children's Hospital, Guangzhou, P. R. China
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24
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Newton BW, Russell WK, Russell DH, Ramaiah SK, Jayaraman A. Liver proteome analysis in a rodent model of alcoholic steatosis. J Proteome Res 2009; 8:1663-71. [PMID: 19714808 DOI: 10.1021/pr800905w] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Alcoholic steatosis (AS) is the initial pathology associated with early stage alcoholic liver disease (ALD) and is characterized by the accumulation of fat in the liver. AS is considered clinically benign because it is reversible, and the progression of AS to alcoholic steatohepatitis (ASH) is a key step in the development of ALD. A two-dimensional gel electrophoresis (2DE)-mass spectrometry (MS) proteomic approach was used to investigate the protein expression pattern underlying AS, as the first step toward determining liver tissue biomarkers for early stage ALD. Several proteins involved in fatty acid and amino acid metabolism were up-regulated in 3- and 6-week ethanol-fed rats relative to isocaloric controls, which suggest a higher energy demand upon chronic exposure to ethanol. In addition, the expression of two proteins associated with alcohol-induced oxidative stress, peroxiredoxin 6 (PRDX6) and aldehyde dehydrogenase 2 (ALDH2), was down-regulated in ethanol fed rats, and suggests an increase in reactive oxygen species and oxidative stress. To investigate if irreversible protein modification arising from oxidative stress during AS impacts protein levels, the extent of carbonylated proteins in the ethanol and isocaloric groups was identified using mass spectrometry. The detection of modified proteins involved in antioxidant functions further supports the notion that oxidative modification of these proteins leads to protein turnover during AS. In addition, the carbonylation of betaine-homocysteine S-methyltransferase, a protein implicated in fatty liver development, in 3-week and 6-week ethanol exposed samples suggests that this protein could be a marker for early stage AS.
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Affiliation(s)
- Billy W Newton
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, USA
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25
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Rithidech KN, Honikel L, Rieger R, Xie W, Rithidech KN, Honikel L, Rieger R, Xie W, Fischer T, Simon SR. Protein-expression profiles in mouse blood-plasma following acute whole-body exposure to137Cs γ rays. Int J Radiat Biol 2009; 85:432-47. [DOI: 10.1080/09553000902820390] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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26
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Chung MC, Jorgensen SC, Popova TG, Tonry JH, Bailey CL, Popov SG. Activation of plasminogen activator inhibitor implicates protease InhA in the acute-phase response to Bacillus anthracis infection. J Med Microbiol 2009; 58:737-744. [PMID: 19429749 DOI: 10.1099/jmm.0.007427-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Anthrax is a zoonotic disease caused by Bacillus anthracis. The infection is associated with inflammation and sepsis, but little is known about the acute-phase response during disease and the nature of the bacterial factors causing it. In this study, we examined the levels of the acute-phase proteins (APPs) in comparative experiments using mice challenged with spores and a purified B. anthracis protease InhA as a possible factor mediating the response. A strong increase in the plasma levels of APPs such as haptoglobin and serum amyloid A was observed during infection. Protein and mRNA levels of plasminogen activator inhibitor (PAI)-1 in the liver were also increased concurrently with bacterial dissemination at 72 h post-infection. Similar effects were observed at 6 h post injection with InhA. Induction of hepatic transforming growth factor-beta1, a PAI-1 inducer, was also found in the liver of InhA-injected mice. PAI-1 elevation by InhA resulted in an increased level of urokinase-type plasminogen activator complex with PAI-1 and a decreased level of D-dimers indicating inhibition of blood fibrinolysis. These results reveal an acute liver response to anthrax infection and provide a plausible pathophysiological link between the host inflammatory response and the pro-thrombotic haemostatic imbalance in the course of disease through PAI-1 induction in the liver.
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Affiliation(s)
- Myung-Chul Chung
- National Center for Biodefense and Infectious Diseases, George Mason University, 10900 University Blvd, Manassas, VA 20110, USA
| | - Shelley C Jorgensen
- National Center for Biodefense and Infectious Diseases, George Mason University, 10900 University Blvd, Manassas, VA 20110, USA
| | - Taissia G Popova
- National Center for Biodefense and Infectious Diseases, George Mason University, 10900 University Blvd, Manassas, VA 20110, USA
| | - Jessica H Tonry
- National Center for Biodefense and Infectious Diseases, George Mason University, 10900 University Blvd, Manassas, VA 20110, USA
| | - Charles L Bailey
- National Center for Biodefense and Infectious Diseases, George Mason University, 10900 University Blvd, Manassas, VA 20110, USA
| | - Serguei G Popov
- National Center for Biodefense and Infectious Diseases, George Mason University, 10900 University Blvd, Manassas, VA 20110, USA
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27
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Duan X, Berthiaume F, Yarmush DM, Yarmush ML. Dissimilar hepatic protein expression profiles during the acute and flow phases following experimental thermal injury. Proteomics 2009; 9:636-47. [PMID: 19137545 DOI: 10.1002/pmic.200700427] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The liver plays a major role in the early hypometabolic and later hypermetabolic phases after severe burn injury. Proteomic analysis was used to identify altered proteins in liver during these two phases. Sprague-Dawley rats were subjected to a full-thickness dorsal burn injury covering 40% of the total body surface area. Controls consisted of sham-treated animals. Liver tissues were collected on postburn days 1 and 7. The proteomic data show greater production of positive acute phase proteins on day 1 than on day 7. Many antioxidant enzymes were coordinately downregulated on day 1, including the potent biliverdin reductase. These antioxidants were restored and in some cases upregulated on day 7. This opposite trend in the change of antioxidant proteins corroborated our finding of more pronounced oxidative stress on day 1 than on day 7 as measured via protein carbonyl content. The changes of metabolic enzymes on days 1 and 7 were consistent with hypo- and hyper-metabolic states, respectively. Furthermore, a previously unreported decrease in ornithine aminotransferase on day 7 may be a key contributor to the observed increased urinary urea excretion during the hypermetabolic phase. Overall, the many differences in protein expression observed on postburn days 1 and 7 reflect the dissimilar hepatic metabolic patterns during the acute and flow phases following burn injury.
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Affiliation(s)
- Xunbao Duan
- Boston Shriners Burns Hospital Special Shared Facility for Genomics and Proteomics, USA
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28
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Merrick BA, Witzmann FA. The role of toxicoproteomics in assessing organ specific toxicity. EXS 2009; 99:367-400. [PMID: 19157068 DOI: 10.1007/978-3-7643-8336-7_13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Aims of this chapter on the role of toxicoproteomics in assessing organ-specific toxicity are to define the field of toxicoproteomics, describe its development among global technologies, and show potential uses in experimental toxicological research, preclinical testing and mechanistic biological research. Disciplines within proteomics deployed in preclinical research are described as Tier I analysis, involving global protein mapping and protein profiling for differential expression, and Tier II proteomic analysis, including global methods for description of function, structure, interactions and post-translational modification of proteins. Proteomic platforms used in toxicoproteomics research are briefly reviewed. Preclinical toxicoproteomic studies with model liver and kidney toxicants are critically assessed for their contributions toward understanding pathophysiology and in biomarker discovery. Toxicoproteomics research conducted in other organs and tissues are briefly discussed as well. The final section suggests several key developments involving new approaches and research focus areas for the field of toxicoproteomics as a new tool for toxicological pathology.
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Affiliation(s)
- B Alex Merrick
- Laboratory of Respiratory Biology, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, Durham, NC 27709, USA.
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29
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Ritorto MS, Borlak J. A simple and reliable protocol for mouse serum proteome profiling studies by use of two-dimensional electrophoresis and MALDI TOF/TOF mass spectrometry. Proteome Sci 2008; 6:25. [PMID: 18789141 PMCID: PMC2563006 DOI: 10.1186/1477-5956-6-25] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Accepted: 09/12/2008] [Indexed: 11/14/2022] Open
Abstract
Background Unravelling the serum proteome is the subject of intensified research. In this regard, two-dimensional electrophoresis coupled with MALDI MS analysis is still one of the most commonly used method. Despite some improvements, there is the need for better protocols to enable comprehensive identification of serum proteins. Here we report a combination of two proteomic strategies, zoom in acidic and neutral part of 2-D gels and an application of two optimised matrix preparations for MALDI-MS analyses to simplify serum proteome mapping. Results Mouse serum proteins were separated by 2-D electrophoresis at the pH ranges 3–10 and 4–7, respectively. Then in gel tryptic digests were analysed by MALDI-MS. Notably, sample-matrix preparations consisted of either a thin-layer α-ciano-4-hydroxycinnamic acid (CHCA) matrix deposition or a matrix-layer 2,5-dihydroxybenzoic acid (DHB). This enabled an identification of 90 proteins. The herein reported method enhanced identification of proteins by 32% when compared with previously published studies of mouse serum proteins, using the same approaches. Furthermore, experimental improvements of matrix preparations enabled automatic identification of mouse proteins, even when one of the two matrices failed. Conclusion We report a simple and reliable protocol for serum proteome analysis that combines an optimized resolution of 2-D gels spots and improved sample-matrix preparations for MALDI-MS analysis. The protocol allowed automated data acquisition for both CHCA and DHB and simplified the MS data acquisition therefore avoiding time-consuming procedures. The simplicity and reliability of the developed protocol may be applied universally.
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Affiliation(s)
- Maria Stella Ritorto
- Department of Drug Research and Medical Biotechnology, Fraunhofer Institute of Toxicology and Experimental Medicine, Hanover, Germany.
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30
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Merrick BA. Toxicoproteomics: Correlating Tissue and Serum Proteomics in Liver Injury. Clin Proteomics 2008. [DOI: 10.1002/9783527622153.ch24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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31
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Guerranti R, Ogueli IG, Bertocci E, Muzzi C, Aguiyi JC, Cianti R, Armini A, Bini L, Leoncini R, Marinello E, Pagani R. Proteomic analysis of the pathophysiological process involved in the antisnake venom effect of Mucuna pruriens extract. Proteomics 2008; 8:402-12. [PMID: 18203263 DOI: 10.1002/pmic.200700265] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Previously, we reported the antisnake venom properties of a Mucuna pruriens seed extract (MPE) and tested its in vivo efficacy against Echis carinatus venom (EV) in short- (1 injection) and long-term (three weekly injections) treatments. The aim of the present study was to investigate plasma proteome changes associated with MPE treatments and identify proteins responsible for survival of envenomated mice (CHALLENGED mice). Six treatment groups were studied. Three control groups: one saline, one short-term and one long-term MPE treatment. One group received EV alone. Two test groups received EV with either a short-term or long-term MPE treatment (CHALLENGED mice). The plasma from each group was analysed by 2-DE/MALDI-TOF MS. The most significant changes with treatment were: albumin, haptoglobin, fibrinogen, serum amyloid A and serum amyloid P. Most of these changes were explained by EV effects on coagulation, inflammation and haemolysis. However, MPE treatments prevented the EV-induced elevation in HPT. Consequently, HPT levels were similar to controls in the plasma of CHALLENGED mice. The plasma of CHALLENGED mice showed substantial proteomic modifications. This suggests the mechanism of MPE protection involves the activation of counterbalancing processes to compensate for the imbalances caused by EV.
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Affiliation(s)
- Roberto Guerranti
- Department of Internal Medicine, Endocrine-Metabolic Sciences and Biochemistry, University of Siena, Via A. Moro 2, Siena, Italy.
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Abstract
Inter-alpha-trypsin inhibitor family proteins are mainly detected in plasma and urine and comprise the common light chain bikunin and at least 6 closely related heavy chains. The bikunin moiety exhibits protease inhibitory activity and has been studied extensively; however, the heavy chains have been largely overlooked. Recent studies clearly indicate that the heavy chain moieties have important biological functions either in association with or independent of bikunin. Because the heavy chains comprise the main part of the protein structure of this family, it is important to understand their functions. This review summarizes the domain structural features of heavy chains, the heavy chain-interacting molecules identified thus far, and the association of heavy chains with diseases to encourage the discovery of novel heavy chains-interacting molecules and to gain a deeper insight into their functions.
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Affiliation(s)
- Lisheng Zhuo
- Institute for Molecular Science of Medicine, Aichi Medical University, Nagakute, Aichi, Japan
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33
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Carpintero R, Alonso C, Piñeiro M, Iturralde M, Andrés M, Le Potier MF, Madec F, Alava MA, Piñeiro A, Lampreave F. Pig major acute-phase protein and apolipoprotein A-I responses correlate with the clinical course of experimentally induced African Swine Fever and Aujeszky's disease. Vet Res 2007; 38:741-53. [PMID: 17637332 DOI: 10.1051/vetres:2007030] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2006] [Accepted: 04/17/2007] [Indexed: 11/14/2022] Open
Abstract
In the present work, we studied the acute phase protein response after experimental virus infection in pigs. The animals were experimentally infected with African Swine Fever (ASF) or Aujeszky's disease (AD) viruses. The clinical course of ASF infection correlated with increasingly high levels of pig Major Acute-phase Protein (pig-MAP) (mean value of 6 mg/mL on day 6 post infection (p.i.), from 6 to 9 times higher than day 0) and sharp apolipoprotein A-I (apo A-I) decrease (mean value of 0.5 mg/mL, from 4 to 10 times lower than day 0 on day 4 p.i.). AD-clinical signs appeared at day 3 p.i., both in vaccinated (moderate clinical signs) and non-vaccinated pigs (severe outcome within 48 h p.i.). Pig-MAP and apo A-I profiles also followed clinical signs (changing from 0.70 mg/mL to around 3 mg/mL and from around 3 mg/mL to 0.96 mg/mL, respectively in non-vaccinated animals), with minor changes in concentration in the vaccinated group. Haptoglobin levels significantly increased in ASF and AD infected animals (mean maximum values of 2.77 and 3.96 mg/mL, respectively). Minor differences for the C-Reactive Protein in the case of ASF were observed, whereas its concentration increased more than 7 times in AD-infection. The albumin level was not modified in either case. The correlation of clinical signs to our data suggests the potential use of pig-MAP and apo A-I in monitoring infections in swine.
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Affiliation(s)
- Rakel Carpintero
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain
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Smith JC, Lambert JP, Elisma F, Figeys D. Proteomics in 2005/2006: developments, applications and challenges. Anal Chem 2007; 79:4325-43. [PMID: 17477510 DOI: 10.1021/ac070741j] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jeffrey C Smith
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ontario, Canada K1H 8M5
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Kristiansson MH, Bhat VB, Babu IR, Wishnok JS, Tannenbaum SR. Comparative time-dependent analysis of potential inflammation biomarkers in lymphoma-bearing SJL mice. J Proteome Res 2007; 6:1735-44. [PMID: 17388619 PMCID: PMC2532589 DOI: 10.1021/pr060497x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
SJL mice colonized with RcsX lymphoma cells undergo a rapid inflammatory response associated with biological and physiological effects including increased nitric oxide production and mutations in spleen DNA. By 2 weeks postcolonization, these changes were accompanied by both up- and down-regulation of a number of plasma proteins. In the experiments reported here, plasma from individual SJL mice was analyzed at several time-points over the 2-week period to determine if there were sets of proteins whose expression varied in concert and thus might serve as early biomarkers for inflammation-related disorders. Samples were collected just prior to injection of the RcsX cells and then after 4, 8, and 12 days. Albumin and immunoglobulins were depleted, and the samples were resolved by 1D gel electrophoresis. The gels were cut into 20 slices, and the proteins were digested in-gel with trypsin. The digests were treated with iTRAQ reagents and then analyzed using LC/MS/MS. The resulting data were processed with two software packages, that is, ProQuant and Spectrum Mill, and then subjected to K-means cluster analysis (K = 4). The four clusters revealed a set of highly up-regulated proteins, a set of progressively up-regulated proteins, a set with no major changes, and a set that declined. The first cluster included haptoglobin and serum amyloid A; the second included groups with several functions including protease inhibition, cell motility, and transport. The iTRAQ results for a selection of the up-regulated proteins, including haptoglobin, hemopexin, serum amyloid P component, and ceruloplasmin, were confirmed with Western blots. Prominent down-regulated proteins included esterase-1, paraoxonase, and alpha-2-macroglobulin. Approximately 50% of the up-regulated proteins are canonical acute phase proteins, while the remainder are regulated by the Nrf2 transcription factor.
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Affiliation(s)
- Monica H. Kristiansson
- Division of Occupational and Environmental Medicine and Psychiatric, Epidemiology, University Hospital, 221 85 Lund, Sweden
| | - Vadiraja B. Bhat
- Division of Investigative Pathology, 1901 South First Street, Building 205, room 1R33, Temple, Texas 76504
| | - I. Ramesh Babu
- Biological Engineering Division, Massachusetts Institute of Technology, 77 Massachusetts Avenue, room 56-731, Cambridge, MA-02139
| | - John S. Wishnok
- Biological Engineering Division, Massachusetts Institute of Technology, 77 Massachusetts Avenue, room 56-731, Cambridge, MA-02139
| | - Steven R. Tannenbaum
- Biological Engineering Division, Massachusetts Institute of Technology, 77 Massachusetts Avenue, room 56-731, Cambridge, MA-02139
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, room 56-731, Cambridge, MA-02139
- To whom correspondence should be addressed: Steven R. Tannenbaum, Underwood-Prescott Professor of Toxicology, Professor of Chemistry, Biological Engineering Division and Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 56-731A, Cambridge, MA 02139, Phone: (617) 253-3729, Fax: (617) 252-1787,
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Josic D, Clifton JG. Use of monolithic supports in proteomics technology. J Chromatogr A 2007; 1144:2-13. [PMID: 17174320 DOI: 10.1016/j.chroma.2006.11.082] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Revised: 11/26/2006] [Accepted: 11/28/2006] [Indexed: 11/26/2022]
Abstract
An overview on the utilization of monoliths in proteomics technology will be given. Both silica- and polymer-based monoliths have broad use for microseparation of tryptic peptides in reversed-phase (RP) mode before identification by mass spectrometry (MS) or by MS/MS. For two-dimensional (2D) LC separation of peptides before MS or MS/MS analysis, a combination of ion-exchange, usually cation-exchange (CEX) chromatography with RP chromatography on monolithic supports can be employed. Immobilized metal ion affinity chromatography monoliths with immobilized Fe3+-ions are used for the isolation of phosphopeptides. Monoliths with immobilized affinity ligands are usually applied to the rapid separation of proteins and peptides. Miniaturized reactors with immobilized proteolytic enzymes are utilized for rapid on- or offline digestion of isolated proteins or protein mixtures prior to identification by LC-MS/MS. Monoliths also have broad potential for application in sample preparation, prior to further proteomic analyses. Monolithic supports with large pore sizes can be exploited for the isolation of nanoparticles, such as cells, organelles, viruses and protein aggregates. The potential for further adoption of monolithic supports in protein separation and enrichment of low abundance proteins prior to proteolytic digestion and final LC-MS/MS protein identification will be discussed.
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Affiliation(s)
- Djuro Josic
- Proteomics Core, COBRE Center for Cancer Research Development, Rhode Island Hospital, CORO West, One Hoppin St., Providence, RI 02903, USA.
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