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Ocular Proteomics

 

The Ocular Proteomics Laboratory is a core platform in Singapore Eye Research Institute (SERI) and provides expertise and instrumentation in cutting-edge proteomics and metabolomics research. Established in 2004, the Ocular Proteomics Laboratory has focused on application of proteomics to clinical samples from the eye to find new biomarkers and understand the disease. Additionally, we collaborate with other research groups within Singapore Eye Research Institute/Singapore National Eye Centre and offer a broad range of proteomics/metabolomics and biological mass spectrometry (MS) services, including protein identification, quantitative proteomics (iTRAQ, high resolution – MRM, SWATH, etc.), characterisation of post-translational modifications (PTMs), MS-based non-targeted and targeted metabolomics, and drug analysis. Recently we have been asked to participate in the Human Proteome Organisation (HUPO) Eye Proteome project which aims to establish the human eye proteome database.

Facility:

  • AB SCIEX TripleTOF 5600 Mass Spectrometer

  • Dionex UltiMate 3000 RSLCnano system

  • AB SCIEX API 2000 MS/MS system

  • Waters 2695 HPLC system

  • Waters Acquity UPLC I-Class system

Capability:

  • Protein identification (identify proteins from a gel band, or whole proteome)

  • Quantitative proteomics and proteomic profiling (iTRAQ, mTRAQ, high-resolution MRM, SWATH, etc.)

  • Post-translational modification discovery (glycosylation, phosphorylation, acetylation, methylation, etc.)

  • MS-based metabolomics

  • Small molecule quantitation (drug level, targeted metabolomics, etc.)

One of our focuses is on tear fluid proteomics and metabolomics. We believe that tear fluid is a useful source for discovering biomarkers associated with the various components of the lacrimal functional unit because of the close relationship of tears to the disease sites. Recent studies by our group showed that more than 1500 proteins and 60 small molecule metabolites were identified in healthy human tears using the latest proteomics and metabolomics technology. This comprehensive tear composition repertoire can be served as a background for future biomarker research of ocular diseases.

The current biomarker research projects which use tears as the source are:

  • Validation study of tear biomarkers for dry eye

  • Epidemiologic studies of tear proteomics in normal Chinese, Malay and Indian population

  • Tear proteomic profiles in post-LASIK (Laser in-situ keratomileusis) dry eye

  • Effect of glaucoma medication on tear protein profiles and use them as biomarkers to predict the risk of glaucoma surgical failure

  • Tear biomarkers in lacrimal gland tumor

  • Tear proteomic profiles in thyroid eye disease

  • Tear proteomic profiles in keratoconus

Other important proteomics/metabolomics projects include:

  • Integrated “Omics” in ocular important drug-resistance pathogens

  • Circulating biomarkers in diabetic retinopathy using a metabolomics approach

  • Molecular mechanism of myopia and atropine treatment in a mouse model using quantitative proteomics

  • Vitreous proteomic profile in diabetic retinopathy

  1. Chen L, Cheng CY, Choi HW, Ikram MK, Sabanayagam C, Tan GS, Tian DC, Zhang L, Venkatesan G, Tai ES, Wang JJ, Mitchell P, Cheung CM, Beuerman RW, Zhou L*, Chan ECY*, Wong TY*. Plasma Metabonomic Profiling of Diabetic Retinopathy. Diabetes. 2016, Accepted. (IF = 8.474). * Corresponding author.

  2. Chen L, Li J, Guo T, Ghosh S, Koh SK, Tian D, Zhang L, Jia D, Beuerman RW, Aebersold R, Chan EC, Zhou L*. Global Metabonomic and Proteomic Analysis of Human Conjunctival Epithelial Cells (IOBA-NHC) in Response to Hyperosmotic Stress. Journal of Proteome Research. 2015, 14, 3982-3995. (IF = 5.001). *Corresponding author.

  3. Tong L, Zhou XY, Jylha A, Aapola U, Liu DN, Koh SK, Tian D, Quah J, Uusitalo H, Beuerman RW, Zhou L*. Quantitation of 47 Human Tear Proteins using High Resolution Multiple Reaction Monitoring (HR-MRM) Based-Mass Spectrometry. Journal of Proteomics. 2015, 115, 36-48. (IF =5.080). *Corresponding author.

  4. Barathi VA, Chaurasia SS, Poidinger M, Koh SK, Tian D, Ho C, Iuvone MP, Beuerman RW, Zhou L*. Involvement of GABA transporters in Atropine-treated Myopic Retina as revealed by iTRAQ Quantitative Proteomics. Journal of Proteome Research. 2014, Nov. 7; 13(11): 4647-4658. (IF = 5.001). *Corresponding author.

  5. Zhou L*, Wei Ruihua, Zhao Ping, Koh Siew Kwan, Beuerman Roger W, Ding Chuanqing, Proteomic Analysis Revealed the Altered Tear Protein Profile in a Rabbit Model of Sjögren’s Syndrome-Associated Dry Eye. Proteomics, 2013, 13(16), 2469-2481. *Corresponding author.

  6. Zhou L, Beuerman RW. Tear analysis in ocular surface diseases. Progress in Retinal and Eye Research, 2012, 31(6), 527-550. (IF = 11.207).

  7. Zhou L*, Zhao SZ, Koh SK, Chen L, Vaz C, Tanavde V, Li XR, Beuerman RW. In-depth analysis of the human tear proteome. Journal of Proteomics, 2012, 75(13), 3877-3885. (IF = 5.080). *Corresponding author.

  8. Chen L, Zhou L*, Chan E, Neo J, Beuerman, RW, Characterization of The Human Tear Metabolome by LC-MS/MS. Journal of Proteome Research. 2011, Oct 7;10(10):4876-82. (IF = 5.617). *Corresponding author.

  9. Wong TT, Zhou L, Li J, Tong L, Zhao SZ, Li XR, Yu SJ, Koh SK, Beuerman RW, Proteomic profiling of inflammatory signaling molecules in the tears of patients on chronic glaucoma medication, Invest. Ophthalmol. Vis. Sci. 2011, Sep 22;52(10):7385-91. (IF = 3.933).

  10. Zhou L, Liu SP, Li J, Ong LB, Guo L, Wohland T, Tang C, Lakshminarayanan R, Mavinahalli J, Verma C, Beuerman RW. The structural parameters to antimicrobial activity, human epithelia cell cytotoxicity and killing mechanism of 10-AA synthetic analogues and covalent dimer derived from hBD3 C-terminal. Amino Acids. 2011 Jan;40(1):123-33. (IF = 4.106).

  11. Zhou L, Beuerman RW, Chew AP, Koh SK, Cafaro TA, Urrets-Zavalia EA, Urrets-Zavalia JA, Li SFY, Serra HM. Quantitative Analysis of N-linked Glycoproteins in Tear Fluid of Climatic Droplet Keratopathy by Glycopeptide Capture and iTRAQ. Journal of Proteome Research, 2009, 8(4), 1992-2003. (IF = 5.737).

  12. Zhou L, Beuerman RW, Chan CM, Zhao SZ, Li XR, Yang H, Tong L, Liu SP, Stern ME, Tan DTH. Identification of Tear Fluid Biomarkers in Dry Eye Syndrome Using iTRAQ Quantitative Proteomics. Journal of Proteome Research, 2009, 8(11), 4889-4905. (IF = 5.737).


Head: Dr Zhou Lei
Contact Us: zhou.lei@seri.com.sg