Transition from Identity to Bioactivity-guided Proteomics for Biomarker Discovery with Focus on the PF2D Platform

Overview

Journal Proteomics Clin Appl

Specialty Biochemistry

Date 2015 Jul 23

PMID 26201056

Citations 1

Authors

Antoine Menoret

Stephen J Crocker

Annabelle Rodriguez

Vijay A Rathinam

Robert B Clark

Anthony T Vella

Affiliations

Soon will be listed here.

Abstract

Proteomic strategies provide a valuable tool kit to identify proteins involved in diseases. With recent progress in MS technology, high throughput proteomics has accelerated protein identification for potential biomarkers. Numerous biomarker candidates have been identified in several diseases, and many are common among pathologies. An overall strategy that could complement and strengthen the search for biomarkers is combining protein identity with biological outcomes. This review describes an emerging framework of bridging bioactivity to protein identity, exploring the possibility that some biomarkers will have a mechanistic role in the disease process. A review of pulmonary, cardiovascular, and CNS biomarkers will be discussed to demonstrate the utility of combining bioactivity with identification as a means to not only find meaningful biomarkers, but also to uncover functional mediators of disease.

Citing Articles

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Sutter P, Willis C, Menoret A, Nicaise A, Sacino A, Sikkema A Proc Natl Acad Sci U S A. 2024; 121(5):e2306816121.

PMID: 38266047 PMC: 10835138. DOI: 10.1073/pnas.2306816121.

References

Shoenfeld Y, Sherer Y, Harats D . Artherosclerosis as an infectious, inflammatory and autoimmune disease. Trends Immunol. 2001; 22(6):293-5. DOI: 10.1016/s1471-4906(01)01922-6. View

Yano H, Kuroda S, Buchanan B . Disulfide proteome in the analysis of protein function and structure. Proteomics. 2002; 2(9):1090-6. DOI: 10.1002/1615-9861(200209)2:9<1090::AID-PROT1090>3.0.CO;2-1. View

Kim J, Mastronardi F, Wood D, Lubman D, Zand R, Moscarello M . Multiple sclerosis: an important role for post-translational modifications of myelin basic protein in pathogenesis. Mol Cell Proteomics. 2003; 2(7):453-62. DOI: 10.1074/mcp.M200050-MCP200. View

Jensen O . Modification-specific proteomics: characterization of post-translational modifications by mass spectrometry. Curr Opin Chem Biol. 2004; 8(1):33-41. DOI: 10.1016/j.cbpa.2003.12.009. View

Speers A, Cravatt B . Profiling enzyme activities in vivo using click chemistry methods. Chem Biol. 2004; 11(4):535-46. DOI: 10.1016/j.chembiol.2004.03.012. View

Signor L, Tigani B, Beckmann N, Falchetto R, Stoeckli M . Two-dimensional electrophoresis protein profiling and identification in rat bronchoalveolar lavage fluid following allergen and endotoxin challenge. Proteomics. 2004; 4(7):2101-10. DOI: 10.1002/pmic.200300727. View

Dumont D, Noben J, Raus J, Stinissen P, Robben J . Proteomic analysis of cerebrospinal fluid from multiple sclerosis patients. Proteomics. 2004; 4(7):2117-24. DOI: 10.1002/pmic.200300715. View

Almeras L, Lefranc D, Drobecq H, De Seze J, Dubucquoi S, Vermersch P . New antigenic candidates in multiple sclerosis: identification by serological proteome analysis. Proteomics. 2004; 4(7):2184-94. DOI: 10.1002/pmic.200300732. View

Hammack B, Y C Fung K, Hunsucker S, Duncan M, Burgoon M, Owens G . Proteomic analysis of multiple sclerosis cerebrospinal fluid. Mult Scler. 2004; 10(3):245-60. DOI: 10.1191/1352458504ms1023oa. View

10.

Martin-Ventura J, Duran M, Blanco-Colio L, Meilhac O, Leclercq A, Michel J . Identification by a differential proteomic approach of heat shock protein 27 as a potential marker of atherosclerosis. Circulation. 2004; 110(15):2216-9. DOI: 10.1161/01.CIR.0000136814.87170.B1. View

11.

Kap-Soon N, Do-Youn L, Hak C, Joo W, Lee E, Chan-Wha K . Protein biomarkers in the plasma of workers occupationally exposed to polycyclic aromatic hydrocarbons. Proteomics. 2004; 4(11):3505-13. DOI: 10.1002/pmic.200400964. View

12.

Cargile B, Bundy J, Stephenson Jr J . Potential for false positive identifications from large databases through tandem mass spectrometry. J Proteome Res. 2004; 3(5):1082-5. DOI: 10.1021/pr049946o. View

13.

Norgren N, Sundstrom P, Svenningsson A, Rosengren L, Stigbrand T, Gunnarsson M . Neurofilament and glial fibrillary acidic protein in multiple sclerosis. Neurology. 2004; 63(9):1586-90. DOI: 10.1212/01.wnl.0000142988.49341.d1. View

14.

Soldi M, Sarto C, Valsecchi C, Magni F, Proserpio V, Ticozzi D . Proteome profile of human urine with two-dimensional liquid phase fractionation. Proteomics. 2005; 5(10):2641-7. DOI: 10.1002/pmic.200401269. View

15.

Wang Y, Wu R, Cho K, Shedden K, Barder T, Lubman D . Classification of cancer cell lines using an automated two-dimensional liquid mapping method with hierarchical clustering techniques. Mol Cell Proteomics. 2005; 5(1):43-52. DOI: 10.1074/mcp.T500023-MCP200. View

16.

Sheng S, Chen D, Van Eyk J . Multidimensional liquid chromatography separation of intact proteins by chromatographic focusing and reversed phase of the human serum proteome: optimization and protein database. Mol Cell Proteomics. 2005; 5(1):26-34. DOI: 10.1074/mcp.T500019-MCP200. View

17.

Kim N, Lee Y, Kim H, Joo H, Youm J, Park W . Potential biomarkers for ischemic heart damage identified in mitochondrial proteins by comparative proteomics. Proteomics. 2006; 6(4):1237-49. DOI: 10.1002/pmic.200500291. View

18.

Shin Y, Lee H, Lee J, Paik Y . Proteomic analysis of mammalian basic proteins by liquid-based two-dimensional column chromatography. Proteomics. 2006; 6(4):1143-50. DOI: 10.1002/pmic.200500433. View

19.

Ornstein D, Tyson D . Proteomics for the identification of new prostate cancer biomarkers. Urol Oncol. 2006; 24(3):231-6. DOI: 10.1016/j.urolonc.2005.11.035. View

20.

Hurst R, Kyker K, Dozmorov M, Takemori N, Singh A, Matsumoto H . Proteome-level display by 2-dimensional chromatography of extracellular matrix-dependent modulation of the phenotype of bladder cancer cells. Proteome Sci. 2006; 4:13. PMC: 1534010. DOI: 10.1186/1477-5956-4-13. View