Proteome Profiling of Developing Murine Lens Through Mass Spectrometry

Overview

Journal Invest Ophthalmol Vis Sci

Specialty Ophthalmology

Date 2018 Jan 15

PMID 29332127

Citations 17

Authors

Shahid Y Khan

Muhammad Ali

Firoz Kabir

Santosh Renuse

Chan Hyun Na

C Conover Talbot Jr

Sean F Hackett

S Amer Riazuddin

Affiliations

Soon will be listed here.

Abstract

Purpose: We previously completed a comprehensive profile of the mouse lens transcriptome. Here, we investigate the proteome of the mouse lens through mass spectrometry-based protein sequencing at the same embryonic and postnatal time points.

Methods: We extracted mouse lenses at embryonic day 15 (E15) and 18 (E18) and postnatal day 0 (P0), 3 (P3), 6 (P6), and 9 (P9). The lenses from each time point were preserved in three distinct pools to serve as biological replicates for each developmental stage. The total cellular protein was extracted from the lens, digested with trypsin, and labeled with isobaric tandem mass tags (TMT) for three independent TMT experiments.

Results: A total of 5404 proteins were identified in the mouse ocular lens in at least one TMT set, 4244 in two, and 3155 were present in all three TMT sets. The majority of the proteins exhibited steady expression at all six developmental time points; nevertheless, we identified 39 proteins that exhibited an 8-fold differential (higher or lower) expression during the developmental time course compared to their respective levels at E15. The lens proteome is composed of diverse proteins that have distinct biological properties and functional characteristics, including proteins associated with cataractogenesis and autophagy.

Conclusions: We have established a comprehensive profile of the developing murine lens proteome. This repository will be helpful in identifying critical components of lens development and processes essential for the maintenance of its transparency.

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References

Datiles M, Schumer D, Zigler Jr J, Russell P, Anderson L, Garland D . Two-dimensional gel electrophoretic analysis of human lens proteins. Curr Eye Res. 1992; 11(7):669-77. DOI: 10.3109/02713689209000740. View

Chen J, Ma Z, Jiao X, Fariss R, Kantorow W, Kantorow M . Mutations in FYCO1 cause autosomal-recessive congenital cataracts. Am J Hum Genet. 2011; 88(6):827-838. PMC: 3113247. DOI: 10.1016/j.ajhg.2011.05.008. View

Wang Z, Schey K . Proteomic Analysis of Lipid Raft-Like Detergent-Resistant Membranes of Lens Fiber Cells. Invest Ophthalmol Vis Sci. 2016; 56(13):8349-60. PMC: 4699431. DOI: 10.1167/iovs.15-18273. View

McAvoy J, Chamberlain C, de Iongh R, Hales A, Lovicu F . Lens development. Eye (Lond). 2000; 13 ( Pt 3b):425-37. DOI: 10.1038/eye.1999.117. View

ROBINSON G, Jan J, Kinnis C . Congenital ocular blindness in children, 1945 to 1984. Am J Dis Child. 1987; 141(12):1321-4. DOI: 10.1001/archpedi.1987.04460120087041. View

Elsobky S, Crane A, Margolis M, Carreon T, Bhattacharya S . Review of application of mass spectrometry for analyses of anterior eye proteome. World J Biol Chem. 2014; 5(2):106-14. PMC: 4050106. DOI: 10.4331/wjbc.v5.i2.106. View

Ma Z, Hanson S, Lampi K, David L, Smith D, Smith J . Age-related changes in human lens crystallins identified by HPLC and mass spectrometry. Exp Eye Res. 1998; 67(1):21-30. DOI: 10.1006/exer.1998.0482. View

Shang F, Wilmarth P, Chang M, Liu K, David L, Caceres M . Newborn mouse lens proteome and its alteration by lysine 6 mutant ubiquitin. J Proteome Res. 2014; 13(3):1177-89. PMC: 3993935. DOI: 10.1021/pr400801v. View

Bassnett S, Wilmarth P, David L . The membrane proteome of the mouse lens fiber cell. Mol Vis. 2009; 15:2448-63. PMC: 2786885. View

10.

Shiels A, Bennett T, Hejtmancik J . Cat-Map: putting cataract on the map. Mol Vis. 2010; 16:2007-15. PMC: 2965572. View

11.

Lampi K, Shih M, Ueda Y, Shearer T, David L . Lens proteomics: analysis of rat crystallin sequences and two-dimensional electrophoresis map. Invest Ophthalmol Vis Sci. 2002; 43(1):216-24. View

12.

Jungblut P, Otto A, Favor J, Lowe M, Muller E, Kastner M . Identification of mouse crystallins in 2D protein patterns by sequencing and mass spectrometry. Application to cataract mutants. FEBS Lett. 1998; 435(2-3):131-7. DOI: 10.1016/s0014-5793(98)01053-9. View

13.

Hejtmancik J, Smaoui N . Molecular genetics of cataract. Dev Ophthalmol. 2003; 37:67-82. DOI: 10.1159/000072039. View

14.

Maes E, Valkenborg D, Baggerman G, Willems H, Landuyt B, Schoofs L . Determination of variation parameters as a crucial step in designing TMT-based clinical proteomics experiments. PLoS One. 2015; 10(3):e0120115. PMC: 4361338. DOI: 10.1371/journal.pone.0120115. View

15.

Khan S, Hackett S, Lee M, Pourmand N, Talbot Jr C, Riazuddin S . Transcriptome Profiling of Developing Murine Lens Through RNA Sequencing. Invest Ophthalmol Vis Sci. 2015; 56(8):4919-26. PMC: 4525677. DOI: 10.1167/iovs.14-16253. View

16.

Song S, Landsbury A, Dahm R, Liu Y, Zhang Q, Quinlan R . Functions of the intermediate filament cytoskeleton in the eye lens. J Clin Invest. 2009; 119(7):1837-48. PMC: 2701874. DOI: 10.1172/JCI38277. View

17.

Sugiyama Y, Shelley E, Wen L, Stump R, Shimono A, Lovicu F . Sfrp1 and Sfrp2 are not involved in Wnt/β-catenin signal silencing during lens induction but are required for maintenance of Wnt/β-catenin signaling in lens epithelial cells. Dev Biol. 2013; 384(2):181-93. PMC: 3844297. DOI: 10.1016/j.ydbio.2013.10.008. View

18.

Kyselova Z . Mass spectrometry-based proteomics approaches applied in cataract research. Mass Spectrom Rev. 2011; 30(6):1173-84. DOI: 10.1002/mas.20317. View

19.

Wawersik S, Purcell P, Rauchman M, Dudley A, Robertson E, Maas R . BMP7 acts in murine lens placode development. Dev Biol. 1999; 207(1):176-88. DOI: 10.1006/dbio.1998.9153. View

20.

Lampi K, Ma Z, Hanson S, Azuma M, Shih M, Shearer T . Age-related changes in human lens crystallins identified by two-dimensional electrophoresis and mass spectrometry. Exp Eye Res. 1998; 67(1):31-43. DOI: 10.1006/exer.1998.0481. View