The Spanish biology/disease initiative within the human proteome project: Application to rheumatic diseases

Journal of Proteomics

Volumn 127, Issue , 2015, Pages 406-413

  Ruiz Romero, Cristina ^a,b   Calamia, Valentina ^a   Albar, Juan Pablo ^b   Casal, José Ignacio ^c   Corrales, Fernando J ^d   Fernández Puente, Patricia ^a   Gil, Concha ^b   Mateos, Jesús ^a   Vivanco, Fernando ^b   Blanco, Francisco J ^a,e  

^a UNIVERSITY OF A CORUÑA   (Spain)

^b INSTITUTO DE SALUD CARLOS III   (Spain)

^c CENTRO DE INVESTIGACIONES BIOLÓGICAS   (Spain)

^d UNIVERSITY OF NAVARRA   (Spain)

^e ProteoRed ISCIII Center for Applied Medical Research ^*  (Spain)

Author keywords

Cartilage; Chondrocyte; Human proteome project; Osteoarthritis; Rheumatic diseases; Synovial fluid

Indexed keywords

AGGRECAN; BIOLOGICAL MARKER; CARTILAGE OLIGOMERIC MATRIX PROTEIN; CD11B ANTIGEN; CHITINASE 3 LIKE PROTEIN 1; COMPLEMENT FACTOR D; FIBRONECTIN; LUMICAN; PIGMENT EPITHELIUM DERIVED FACTOR; PROTEIN; PROTEOGLYCAN; PROTEOGLYCAN 4; PROTEOME; TETRANECTIN; THROMBOSPONDIN 1; UNCLASSIFIED DRUG;

ATHEROSCLEROSIS; BRAIN CANCER; BREAST CANCER; CANDIDIASIS; CARDIOVASCULAR DISEASE; CHROMOSOME 16; COLON CANCER; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; HUMAN; INFECTION; NEOPLASM; OBESITY; OSTEOARTHRITIS; PRIORITY JOURNAL; PROTEOMICS; REVIEW; RHEUMATIC DISEASE; RHEUMATOID ARTHRITIS; SYSTEMIC LUPUS ERYTHEMATOSUS; FEMALE; GENETICS; MALE; METABOLISM; PROCEDURES; SPAIN;

CHROMOSOMES, HUMAN, PAIR 16; FEMALE; HUMANS; MALE; OSTEOARTHRITIS; PROTEOME; PROTEOMICS; SPAIN;

EID: 84944149688     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2015.01.023     Document Type: Review

References (47)

1. Legrain P., Aebersold R., Archakov A., Bairoch A., Bala K., Beretta L., et al. The human proteome project: current state and future direction. Mol Cell Proteomics 2011, 10(7):M111. (009993).
2. Paik Y.K., Jeong S.K., Omenn G.S., Uhlen M., Hanash S., Cho S.Y., et al. The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nat Biotechnol 2012, 30(3):221-223.
3. Pritzker K. Pathology of osteoarthritis. Osteoarthritis 1998, 50-61. Oxford University Press, New York. K. Brandt, M. Doherty, L. Lohmander (Eds.).
4. Castro-Santos P., Laborde C.M., Diaz-Pena R. Genomics, proteomics and metabolomics: their emerging roles in the discovery and validation of rheumatoid arthritis biomarkers. Clin Exp Rheumatol 2015, (Epub ahead of print).
5. Ruiz-Romero C., Blanco F.J. Achievements and challenges of proteomics in the study of rheumatoid arthritis. Curr Top Med Chem 2013, 13(6):732-742.
6. Elding H., Lau W., Swallow D.M., Maniatis N. Dissecting the genetics of complex inheritance: linkage disequilibrium mapping provides insight into Crohn disease. Am J Hum Genet 2011, 89(6):798-805.
7. Deng Y., Tsao B.P. Genetic susceptibility to systemic lupus erythematosus in the genomic era. Nat Rev Rheumatol 2010, 6(12):683-692.
8. Nath S.K., Han S., Kim-Howard X., Kelly J.A., Viswanathan P., Gilkeson G.S., et al. A nonsynonymous functional variant in integrin-alpha(M) (encoded by ITGAM) is associated with systemic lupus erythematosus. Nat Genet 2008, 40(2):152-154.
9. Ruiz-Romero C., Blanco F.J. The role of proteomics in osteoarthritis pathogenesis research. Curr Drug Targets 2009, 10(6):543-556.
10. Ruiz-Romero C., Blanco F.J. Proteomics role in the search for improved diagnosis, prognosis and treatment of osteoarthritis. Osteoarthritis Cartilage 2010, 18(4):500-509.
11. Ruiz-Romero C., Carreira V., Rego I., Remeseiro S., Lopez-Armada M.J., Blanco F.J. Proteomic analysis of human osteoarthritic chondrocytes reveals protein changes in stress and glycolysis. Proteomics 2008, 8(3):495-507.
12. Ruiz-Romero C., Calamia V., Rocha B., Mateos J., Fernandez-Puente P., Blanco F.J. Hypoxia conditions differentially modulate human normal and osteoarthritic chondrocyte proteomes. J Proteome Res 2010, 9(6):3035-3045.
13. Cillero-Pastor B., Ruiz-Romero C., Carames B., Lopez-Armada M.J., Blanco F.J. Proteomic analysis by two-dimensional electrophoresis to identify the normal human chondrocyte proteome stimulated by tumor necrosis factor alpha and interleukin-1beta. Arthritis Rheum 2010, 62(3):802-814.
14. Calamia V., Ruiz-Romero C., Rocha B., Fernandez-Puente P., Mateos J., Montell E., et al. Pharmacoproteomic study of the effects of chondroitin and glucosamine sulfate on human articular chondrocytes. Arthritis Res Ther 2010, 12(4):R138.
15. Ruiz-Romero C., Lopez-Armada M.J., Blanco F.J. Mitochondrial proteomic characterization of human normal articular chondrocytes. Osteoarthritis Cartilage 2006, 14(6):507-518.
16. Ruiz-Romero C., Calamia V., Mateos J., Carreira V., Martinez-Gomariz M., Fernandez M., et al. Mitochondrial dysregulation of osteoarthritic human articular chondrocytes analyzed by proteomics: a decrease in mitochondrial superoxide dismutase points to a redox imbalance. Mol Cell Proteomics 2009, 8(1):172-189.
17. Blanco F.J., Rego I., Ruiz-Romero C. The role of mitochondria in osteoarthritis. Nat Rev Rheumatol 2011, 7(3):161-169.
18. Rego I., Fernandez-Moreno M., Fernandez-Lopez C., Gomez-Reino J.J., Gonzalez A., Arenas J., et al. Role of European mitochondrial DNA haplogroups in the prevalence of hip osteoarthritis in Galicia, Northern Spain. Ann Rheum Dis 2010, 69(1):210-213.
19. Calamia V., Rocha B., Mateos J., Fernandez-Puente P., Ruiz-Romero C., Blanco F.J. Metabolic labeling of chondrocytes for the quantitative analysis of the interleukin-1-beta-mediated modulation of their intracellular and extracellular proteomes. J Proteome Res 2011, 10(8):3701-3711.
20. Calamia V., Fernandez-Puente P., Mateos J., Lourido L., Rocha B., Montell E., et al. Pharmacoproteomic study of three different chondroitin sulfate compounds on intracellular and extracellular human chondrocyte proteomes. Mol Cell Proteomics 2012, 11(6):M111. (013417).
21. Calamia V., Lourido L., Fernández-Puente P., Mateos J., Rocha B., Montell E., et al. Secretome analysis of chondroitin sulfate-treated chondrocytes reveals anti-angiogenic, anti-inflammatory and anti-catabolic properties. Arthritis Res Ther 2012, 14(5):R202.
22. Guo D., Tan W., Wang F., Lv Z., Hu J., Lv T., et al. Proteomic analysis of human articular cartilage: identification of differentially expressed proteins in knee osteoarthritis. Joint Bone Spine 2008, 75(4):439-444.
23. Wu J., Liu W., Bemis A., Wang E., Qiu Y., Morris E.A., et al. Comparative proteomic characterization of articular cartilage tissue from normal donors and patients with osteoarthritis. Arthritis Rheum 2007, 56(11):3675-3684.
24. Zhen E.Y., Brittain I.J., Laska D.A., Mitchell P.G., Sumer E.U., Karsdal M.A., et al. Characterization of metalloprotease cleavage products of human articular cartilage. Arthritis Rheum 2008, 58(8):2420-2431.
25. Peffers M.J., Beynon R.J., Clegg P.D. Absolute quantification of selected proteins in the human osteoarthritic secretome. Int J Mol Sci 2013, 14(10):20658-20681.
26. Lourido L., Calamia V., Mateos J., Fernandez-Puente P., Fernandez-Tajes J., Blanco F.J., et al. Quantitative proteomic profiling of human articular cartilage degradation in osteoarthritis. J Proteome Res 2014, 13(12):6096-6106.
27. Lotz M., Martel-Pelletier J., Christiansen C., Brandi M.L., Bruyere O., Chapurlat R., et al. Value of biomarkers in osteoarthritis: current status and perspectives. Ann Rheum Dis 2013, 72(11):1756-1763.
28. de Seny D., Sharif M., Fillet M., Cobraiville G., Meuwis M.A., Maree R., et al. Discovery and biochemical characterisation of four novel biomarkers for osteoarthritis. Ann Rheum Dis 2011, 70(6):1144-1152.
29. Takinami Y., Yoshimatsu S., Uchiumi T., Toyosaki-Maeda T., Morita A., Ishihara T., et al. Identification of potential prognostic markers for knee osteoarthritis by serum proteomic analysis. Biomark Insights 2013, 8:85-95.
30. Fernandez-Puente P., Mateos J., Fernandez-Costa C., Oreiro N., Fernandez-Lopez C., Ruiz-Romero C., et al. Identification of a panel of novel serum osteoarthritis biomarkers. J Proteome Res 2011, 10(11):5095-5101.
31. Mateos J., Lourido L., Fernández-Puente P., Calamia V., Fernández-López C., Oreiro N., et al. Differential protein profiling of synovial fluid from rheumatoid arthritis and osteoarthritis patients using LC-MALDI TOF/TOF. J Proteomics 2012, 75(10):2869-2878.
32. Han M.Y., Dai J.J., Zhang Y., Lin Q., Jiang M., Xu X.Y., et al. Identification of osteoarthritis biomarkers by proteomic analysis of synovial fluid. J Int Med Res 2012, 40(6):2243-2250.
33. Gobezie R., Kho A., Krastins B., Sarracino D.A., Thornhill T.S., Chase M., et al. High abundance synovial fluid proteome: distinct profiles in health and osteoarthritis. Arthritis Res Ther 2007, 9(2):R36.
34. Ritter S.Y., Subbaiah R., Bebek G., Crish J., Scanzello C.R., Krastins B., et al. Proteomic analysis of synovial fluid from the osteoarthritic knee: comparison with transcriptome analyses of joint tissues. Arthritis Rheum 2013, 65(4):981-992.
35. Verma P., Dalal K. Serum cartilage oligomeric matrix protein (COMP) in knee osteoarthritis: a novel diagnostic and prognostic biomarker. J Orthop Res 2013, 31(7):999-1006.
36. Zivanovic S., Rackov L.P., Vojvodic D., Vucetic D. Human cartilage glycoprotein 39-biomarker of joint damage in knee osteoarthritis. Int Orthop 2009, 33(4):1165-1170.
37. Hsueh M.F., Onnerfjord P., Kraus V.B. Biomarkers and proteomic analysis of osteoarthritis. Matrix Biol 2014, 39c:56-66.
38. Bauer D.C., Hunter D.J., Abramson S.B., Attur M., Corr M., Felson D., et al. Classification of osteoarthritis biomarkers: a proposed approach. Osteoarthritis Cartilage 2006, 14(8):723-727.
39. Kraus V.B., Burnett B., Coindreau J., Cottrell S., Eyre D., Gendreau M., et al. Application of biomarkers in the development of drugs intended for the treatment of osteoarthritis. Osteoarthritis Cartilage 2011, 19(5):515-542.
40. Aebersold R., Bader G.D., Edwards A.M., van Eyk J.E., Kussmann M., Qin J., et al. The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community. J Proteome Res 2013, 12(1):23-27.
41. Surinova S., Huttenhain R., Chang C.Y., Espona L., Vitek O., Aebersold R. Automated selected reaction monitoring data analysis workflow for large-scale targeted proteomic studies. Nat Protoc 2013, 8(8):1602-1619.
42. Liu Y., Huttenhain R., Collins B., Aebersold R. Mass spectrometric protein maps for biomarker discovery and clinical research. Expert Rev Mol Diagn 2013, 13(8):811-825.
43. Ritter S.Y., Collins J., Krastins B., Sarracino D., Lopez M., Losina E., et al. Mass spectrometry assays of plasma biomarkers to predict radiographic progression of knee osteoarthritis. Arthritis Res Ther 2014, 16(5):456.
44. Fagerberg L., Oksvold P., Skogs M., Algenas C., Lundberg E., Ponten F., et al. Contribution of antibody-based protein profiling to the human Chromosome-centric Proteome Project (C-HPP). J Proteome Res 2013, 12(6):2439-2448.
45. Chandra P.E., Sokolove J., Hipp B.G., Lindstrom T.M., Elder J.T., Reveille J.D., et al. Novel multiplex technology for diagnostic characterization of rheumatoid arthritis. Arthritis Res Ther 2011, 13(3):R102.
46. Henjes F., Lourido L., Ruiz-Romero C., Fernandez-Tajes J., Schwenk J.M., Gonzalez-Gonzalez M., et al. Analysis of autoantibody profiles in osteoarthritis using comprehensive protein array concepts. J Proteome Res 2014, 13(11):5218-5229.
47. Uhlen M., Oksvold P., Fagerberg L., Lundberg E., Jonasson K., Forsberg M., et al. Towards a knowledge-based human protein atlas. Nat Biotechnol 2010, 28(12):1248-1250.