Multiplexed mass spectrometry monitoring of biomarker candidates for osteoarthritis

Journal of Proteomics - Tập 152 - Trang 216-225 - 2017
Patricia Fernández-Puente1, Valentina Calamia1, Lucía González-Rodríguez1, Lucía Lourido1, María Camacho-Encina1, Natividad Oreiro1, Cristina Ruiz-Romero1,2, Francisco J Blanco1,3
1Proteomics Group-PBR2-ProteoRed/ISCIII, Rheumatology Division, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), As Xubias, 84, 15006 A Coruña, Spain
2CIBER-BBN Instituto de Salud Carlos III, INIBIC-CHUAC, As Xubias 84, 15006 A Coruña, Spain
3RIER-RED de Inflamación y Enfermedades Reumáticas, INIBIC-CHUAC, As Xubias 84, 15006 A Coruña, Spain

Tài liệu tham khảo

Segura, 2014, Surfing transcriptomic landscapes. A step beyond the annotation of Chromosome 16 proteome, J. Proteome Res., 13, 158, 10.1021/pr400721r Ruiz-Romero, 2015, The Spanish biology/disease initiative within the human proteome project: application to rheumatic diseases, J. Proteome, 127, 406, 10.1016/j.jprot.2015.01.023 Cooper, 2013, How to define responders in osteoarthritis, Curr. Med. Res. Opin., 29, 719, 10.1185/03007995.2013.792793 Hunter, 2014, Biomarkers for osteoarthritis: current position and steps towards further validation, Best Pract. Res. Clin. Rheumatol., 28, 61, 10.1016/j.berh.2014.01.007 Kraus, 2015, Call for standardized definitions of osteoarthritis and risk stratification for clinical trials and clinical use, Osteoarthr. Cartil., 23, 1233, 10.1016/j.joca.2015.03.036 Ruiz-Romero, 2015, Lessons from the proteomic study of osteoarthritis, Expert Rev. Proteomics, 12, 433, 10.1586/14789450.2015.1065182 Lotz, 2013, Value of biomarkers in osteoarthritis: current status and perspectives, Ann. Rheum. Dis., 72, 1756, 10.1136/annrheumdis-2013-203726 Aebersold, 2013, The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community, J. Proteome Res., 12, 23, 10.1021/pr301151m Ritter, 2013, Proteomic analysis of synovial fluid from the osteoarthritic knee: comparison with transcriptome analyses of joint tissues, Arthritis Rheum., 65, 981, 10.1002/art.37823 Henjes, 2014, Analysis of autoantibody profiles in osteoarthritis using comprehensive protein array concepts, J. Proteome Res., 13, 5218, 10.1021/pr500775a Fernandez-Puente, 2011, Identification of a panel of novel serum osteoarthritis biomarkers, J. Proteome Res., 10, 5095, 10.1021/pr200695p Finger, 2003, Molecular phenotyping of human chondrocyte cell lines T/C-28a2, T/C-28a4, and C-28/I2, Arthritis Rheum., 48, 3395, 10.1002/art.11341 Altman, 1986, Development of criteria for the classification and reporting of osteoarthritis. Classification of osteoarthritis of the knee. Diagnostic and Therapeutic Criteria Committee of the American Rheumatism Association, Arthritis Rheum., 29, 1039, 10.1002/art.1780290816 Kessler, 1998, Scoring prevalence and severity in gonarthritis: the suitability of the Kellgren & Lawrence scale, Clin. Rheumatol., 17, 205, 10.1007/BF01451048 Bradford, 1976, A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding, Anal. Biochem., 72, 248, 10.1016/0003-2697(76)90527-3 Desjardins, 2009, Microvolume protein concentration determination using the NanoDrop 2000c spectrophotometer, J. Vis. Exp., 10.3791/1610 MacLean, 2010, Skyline: an open source document editor for creating and analyzing targeted proteomics experiments, Bioinformatics, 26, 966, 10.1093/bioinformatics/btq054 Craig, 2004, Open source system for analyzing, validating, and storing protein identification data, J. Proteome Res., 3, 1234, 10.1021/pr049882h Percy, 2014, Enhanced sensitivity and multiplexing with 2D LC/MRM-MS and labeled standards for deeper and more comprehensive protein quantitation, J. Proteome, 106, 113, 10.1016/j.jprot.2014.04.024 Ruiz-Romero, 2008, Proteomic analysis of human osteoarthritic chondrocytes reveals protein changes in stress and glycolysis, Proteomics, 8, 495, 10.1002/pmic.200700249 Lourido, 2014, Quantitative proteomic profiling of human articular cartilage degradation in osteoarthritis, J. Proteome Res., 13, 6096, 10.1021/pr501024p Mateos, 2012, Differential protein profiling of synovial fluid from rheumatoid arthritis and osteoarthritis patients using LC-MALDI TOF/TOF, J. Proteome, 75, 2869, 10.1016/j.jprot.2011.12.042 Fernandez-Costa, 2012, Sequential depletion of human serum for the search of osteoarthritis biomarkers, Proteome Sci., 10, 55, 10.1186/1477-5956-10-55 Calamia, 2011, Metabolic labeling of chondrocytes for the quantitative analysis of the interleukin-1-beta-mediated modulation of their intracellular and extracellular proteomes, J. Proteome Res., 10, 3701, 10.1021/pr200331k Wang, 2011, Identification of a central role for complement in osteoarthritis, Nat. Med., 17, 1674, 10.1038/nm.2543 Blankley, 2013, A label-free selected reaction monitoring workflow identifies a subset of pregnancy specific glycoproteins as potential predictive markers of early-onset pre-eclampsia, Mol. Cell. Proteomics, 12, 3148, 10.1074/mcp.M112.026872 Carr, 2014, Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach, Mol. Cell. Proteomics, 13, 907, 10.1074/mcp.M113.036095 Aguilar-Mahecha, 2012, The effect of pre-analytical variability on the measurement of MRM-MS-based mid- to high-abundance plasma protein biomarkers and a panel of cytokines, PLoS One, 7, 10.1371/journal.pone.0038290 Lopez, 2010, Selected reaction monitoring-mass spectrometric immunoassay responsive to parathyroid hormone and related variants, Clin. Chem., 56, 281, 10.1373/clinchem.2009.137323 Percy, 2013, Standardized protocols for quality control of MRM-based plasma proteomic workflows, J. Proteome Res., 12, 222, 10.1021/pr300893w Percy, 2014, Multiplexed MRM with internal standards for cerebrospinal fluid candidate protein biomarker quantitation, J. Proteome Res., 13, 3733, 10.1021/pr500317d Chambers, 2015, Multiple reaction monitoring enables precise quantification of 97 proteins in dried blood spots, Mol. Cell. Proteomics, 14, 3094, 10.1074/mcp.O115.049957 Wehr, 2012, Relative quantification of serum proteins from pancreatic ductal adenocarcinoma patients by stable isotope dilution liquid chromatography-mass spectrometry, J. Proteome Res., 11, 1749, 10.1021/pr201011f Tsunezumi, 2009, Matrilysin (MMP-7) cleaves C-type lectin domain family 3 member A (CLEC3A) on tumor cell surface and modulates its cell adhesion activity, J. Cell. Biochem., 106, 693, 10.1002/jcb.22062 Chambers, 2013, Comparison of proteins in whole blood and dried blood spot samples by LC/MS/MS, J. Am. Soc. Mass Spectrom., 24, 1338, 10.1007/s13361-013-0678-x Kennedy, 2014, Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins, Nat. Methods, 11, 149, 10.1038/nmeth.2763 Brownridge, 2011, The importance of the digest: proteolysis and absolute quantification in proteomics, Methods, 54, 351, 10.1016/j.ymeth.2011.05.005 Arsene, 2008, Protein quantification by isotope dilution mass spectrometry of proteolytic fragments: cleavage rate and accuracy, Anal. Chem., 80, 4154, 10.1021/ac7024738 Kamiie, 2008, Quantitative atlas of membrane transporter proteins: development and application of a highly sensitive simultaneous LC/MS/MS method combined with novel in-silico peptide selection criteria, Pharm. Res., 25, 1469, 10.1007/s11095-008-9532-4 Gutteridge, 1987, The antioxidant activity of haptoglobin towards haemoglobin-stimulated lipid peroxidation, Biochim. Biophys. Acta, 917, 219, 10.1016/0005-2760(87)90125-1 Nielsen, 2009, Receptor targeting of hemoglobin mediated by the haptoglobins: roles beyond heme scavenging, Blood, 114, 764, 10.1182/blood-2009-01-198309 Arredouani, 2003, Haptoglobin directly affects T cells and suppresses T helper cell type 2 cytokine release, Immunology, 108, 144, 10.1046/j.1365-2567.2003.01569.x Kume, 2014, Discovery of colorectal cancer biomarker candidates by membrane proteomic analysis and subsequent verification using selected reaction monitoring (SRM) and tissue microarray (TMA) analysis, Mol. Cell. Proteomics, 13, 1471, 10.1074/mcp.M113.037093 Ritter, 2014, Mass spectrometry assays of plasma biomarkers to predict radiographic progression of knee osteoarthritis, Arthritis Res. Ther., 16, 456, 10.1186/s13075-014-0456-6 Hsueh, 2014, Biomarkers and proteomic analysis of osteoarthritis, Matrix Biol., 39c, 56, 10.1016/j.matbio.2014.08.012 Lenting, 2012, Von Willebrand factor: the old, the new and the unknown, J. Thromb. Haemost., 10, 2428, 10.1111/jth.12008 Ohshima, 2003, Galectin 3 and its binding protein in rheumatoid arthritis, Arthritis Rheum., 48, 2788, 10.1002/art.11287 Pfander, 2000, Expression of thrombospondin-1 and its receptor CD36 in human osteoarthritic cartilage, Ann. Rheum. Dis., 59, 448, 10.1136/ard.59.6.448 Duncan, 2009, Quantifying proteins by mass spectrometry: the selectivity of SRM is only part of the problem, Proteomics, 9, 1124, 10.1002/pmic.200800739 Muttigi, 2016, Matrilin-3 role in cartilage development and osteoarthritis, Int. J. Mol. Sci., 17, 590, 10.3390/ijms17040590 Klatt, 2013, The matrilin-3 VWA1 domain modulates interleukin-6 release from primary human chondrocytes, Osteoarthr. Cartil., 21, 869, 10.1016/j.joca.2013.03.005 Nakajima, 2011, Cloning and characterization of the osteoarthritis-associated gene DVWA, J. Bone Miner. Metab., 29, 300, 10.1007/s00774-010-0230-z Zhang, 2015, Association between genetic variants of DVWA and osteoarthritis of the knee and hip: a comprehensive meta-analysis, Int. J. Clin. Exp. Med., 8, 9430 Wang, 2016, Single nucleotide polymorphisms and osteoarthritis: an overview and a meta-analysis, Medicine (Baltimore), 95 Veselinovic, 2012, Carotid enlargement and serum levels of von Willebrand factor in rheumatoid arthritis: a follow-up study, Clin. Rheumatol., 31, 1727, 10.1007/s10067-012-2079-0 Ogdie, 2010, Identification of broadly discriminatory tissue biomarkers of synovitis with binary and multicategory receiver operating characteristic analysis, Biomarkers, 15, 183, 10.3109/13547500903411095