Proteome-transcriptome analysis and proteome remodeling in mouse lens epithelium and fibers

Yilin Zhao, Phillip A. Wilmarth, Catherine Cheng, Saima Limi, Velia M. Fowler, Deyou Zheng, Larry L. David, Ales Cvekl

Research output: Contribution to journalArticle

Abstract

Epithelial cells and differentiated fiber cells represent distinct compartments in the ocular lens. While previous studies have revealed proteins that are preferentially expressed in epithelial vs. fiber cells, a comprehensive proteomics library comparing the molecular compositions of epithelial vs. fiber cells is essential for understanding lens formation, function, disease and regenerative potential, and for efficient differentiation of pluripotent stem cells for modeling of lens development and pathology in vitro. To compare protein compositions between the lens epithelium and fibers, we employed tandem mass spectrometry (2D-LC/MS) analysis of microdissected mouse P0.5 lenses. Functional classifications of the top 525 identified proteins into gene ontology categories by molecular processes and subcellular localizations, were adapted for the lens. Expression levels of both epithelial and fiber proteomes were compared with whole lens proteome and mRNA levels using E14.5, E16.5, E18.5, and P0.5 RNA-Seq data sets. During this developmental time window, multiple complex biosynthetic and catabolic processes generate the molecular and structural foundation for lens transparency. As expected, crystallins showed a high correlation between their mRNA and protein levels. Comprehensive data analysis confirmed and/or predicted roles for transcription factors (TFs), RNA-binding proteins (e.g. Carhsp1), translational apparatus including ribosomal heterogeneity and initiation factors, microtubules, cytoskeletal [e.g. non-muscle myosin IIA heavy chain (Myh9) and βB2-spectrin (Sptbn2)] and membrane proteins in lens formation and maturation. Our data highlighted many proteins with unknown functions in the lens that were preferentially enriched in epithelium or fibers, setting the stage for future studies to further dissect the roles of these proteins in fiber cell differentiation vs. epithelial cell maintenance. In conclusion, the present proteomic datasets represent the first mouse lens epithelium and fiber cell proteomes, establish comparative analyses of protein and RNA-Seq data, and characterize the major proteome remodeling required to form the mature lens fiber cells.

LanguageEnglish (US)
Pages32-46
Number of pages15
JournalExperimental Eye Research
Volume179
DOIs
StatePublished - Feb 1 2019

Fingerprint

Gene Expression Profiling
Proteome
Lenses
Epithelium
Proteins
Proteomics
Nonmuscle Myosin Type IIA
Epithelial Cells
RNA
Spectrin
Peptide Initiation Factors
Pluripotent Stem Cells
Messenger RNA
Crystalline Lens
Crystallins
Gene Ontology
RNA-Binding Proteins
Myosin Heavy Chains
Tandem Mass Spectrometry
Microtubules

Keywords

  • Differentiation
  • Lens
  • Mass spectrometry
  • Proteome
  • RNA-Seq
  • Transcription factors
  • Transcriptome

ASJC Scopus subject areas

  • Ophthalmology
  • Sensory Systems
  • Cellular and Molecular Neuroscience

Cite this

Proteome-transcriptome analysis and proteome remodeling in mouse lens epithelium and fibers. / Zhao, Yilin; Wilmarth, Phillip A.; Cheng, Catherine; Limi, Saima; Fowler, Velia M.; Zheng, Deyou; David, Larry L.; Cvekl, Ales.

In: Experimental Eye Research, Vol. 179, 01.02.2019, p. 32-46.

Research output: Contribution to journalArticle

Zhao, Yilin ; Wilmarth, Phillip A. ; Cheng, Catherine ; Limi, Saima ; Fowler, Velia M. ; Zheng, Deyou ; David, Larry L. ; Cvekl, Ales. / Proteome-transcriptome analysis and proteome remodeling in mouse lens epithelium and fibers. In: Experimental Eye Research. 2019 ; Vol. 179. pp. 32-46.
@article{67075b1ab8eb42b3aebe3b33494da561,
title = "Proteome-transcriptome analysis and proteome remodeling in mouse lens epithelium and fibers",
abstract = "Epithelial cells and differentiated fiber cells represent distinct compartments in the ocular lens. While previous studies have revealed proteins that are preferentially expressed in epithelial vs. fiber cells, a comprehensive proteomics library comparing the molecular compositions of epithelial vs. fiber cells is essential for understanding lens formation, function, disease and regenerative potential, and for efficient differentiation of pluripotent stem cells for modeling of lens development and pathology in vitro. To compare protein compositions between the lens epithelium and fibers, we employed tandem mass spectrometry (2D-LC/MS) analysis of microdissected mouse P0.5 lenses. Functional classifications of the top 525 identified proteins into gene ontology categories by molecular processes and subcellular localizations, were adapted for the lens. Expression levels of both epithelial and fiber proteomes were compared with whole lens proteome and mRNA levels using E14.5, E16.5, E18.5, and P0.5 RNA-Seq data sets. During this developmental time window, multiple complex biosynthetic and catabolic processes generate the molecular and structural foundation for lens transparency. As expected, crystallins showed a high correlation between their mRNA and protein levels. Comprehensive data analysis confirmed and/or predicted roles for transcription factors (TFs), RNA-binding proteins (e.g. Carhsp1), translational apparatus including ribosomal heterogeneity and initiation factors, microtubules, cytoskeletal [e.g. non-muscle myosin IIA heavy chain (Myh9) and βB2-spectrin (Sptbn2)] and membrane proteins in lens formation and maturation. Our data highlighted many proteins with unknown functions in the lens that were preferentially enriched in epithelium or fibers, setting the stage for future studies to further dissect the roles of these proteins in fiber cell differentiation vs. epithelial cell maintenance. In conclusion, the present proteomic datasets represent the first mouse lens epithelium and fiber cell proteomes, establish comparative analyses of protein and RNA-Seq data, and characterize the major proteome remodeling required to form the mature lens fiber cells.",
keywords = "Differentiation, Lens, Mass spectrometry, Proteome, RNA-Seq, Transcription factors, Transcriptome",
author = "Yilin Zhao and Wilmarth, {Phillip A.} and Catherine Cheng and Saima Limi and Fowler, {Velia M.} and Deyou Zheng and David, {Larry L.} and Ales Cvekl",
year = "2019",
month = "2",
day = "1",
doi = "10.1016/j.exer.2018.10.011",
language = "English (US)",
volume = "179",
pages = "32--46",
journal = "Experimental Eye Research",
issn = "0014-4835",
publisher = "Academic Press Inc.",

}

TY - JOUR

T1 - Proteome-transcriptome analysis and proteome remodeling in mouse lens epithelium and fibers

AU - Zhao, Yilin

AU - Wilmarth, Phillip A.

AU - Cheng, Catherine

AU - Limi, Saima

AU - Fowler, Velia M.

AU - Zheng, Deyou

AU - David, Larry L.

AU - Cvekl, Ales

PY - 2019/2/1

Y1 - 2019/2/1

N2 - Epithelial cells and differentiated fiber cells represent distinct compartments in the ocular lens. While previous studies have revealed proteins that are preferentially expressed in epithelial vs. fiber cells, a comprehensive proteomics library comparing the molecular compositions of epithelial vs. fiber cells is essential for understanding lens formation, function, disease and regenerative potential, and for efficient differentiation of pluripotent stem cells for modeling of lens development and pathology in vitro. To compare protein compositions between the lens epithelium and fibers, we employed tandem mass spectrometry (2D-LC/MS) analysis of microdissected mouse P0.5 lenses. Functional classifications of the top 525 identified proteins into gene ontology categories by molecular processes and subcellular localizations, were adapted for the lens. Expression levels of both epithelial and fiber proteomes were compared with whole lens proteome and mRNA levels using E14.5, E16.5, E18.5, and P0.5 RNA-Seq data sets. During this developmental time window, multiple complex biosynthetic and catabolic processes generate the molecular and structural foundation for lens transparency. As expected, crystallins showed a high correlation between their mRNA and protein levels. Comprehensive data analysis confirmed and/or predicted roles for transcription factors (TFs), RNA-binding proteins (e.g. Carhsp1), translational apparatus including ribosomal heterogeneity and initiation factors, microtubules, cytoskeletal [e.g. non-muscle myosin IIA heavy chain (Myh9) and βB2-spectrin (Sptbn2)] and membrane proteins in lens formation and maturation. Our data highlighted many proteins with unknown functions in the lens that were preferentially enriched in epithelium or fibers, setting the stage for future studies to further dissect the roles of these proteins in fiber cell differentiation vs. epithelial cell maintenance. In conclusion, the present proteomic datasets represent the first mouse lens epithelium and fiber cell proteomes, establish comparative analyses of protein and RNA-Seq data, and characterize the major proteome remodeling required to form the mature lens fiber cells.

AB - Epithelial cells and differentiated fiber cells represent distinct compartments in the ocular lens. While previous studies have revealed proteins that are preferentially expressed in epithelial vs. fiber cells, a comprehensive proteomics library comparing the molecular compositions of epithelial vs. fiber cells is essential for understanding lens formation, function, disease and regenerative potential, and for efficient differentiation of pluripotent stem cells for modeling of lens development and pathology in vitro. To compare protein compositions between the lens epithelium and fibers, we employed tandem mass spectrometry (2D-LC/MS) analysis of microdissected mouse P0.5 lenses. Functional classifications of the top 525 identified proteins into gene ontology categories by molecular processes and subcellular localizations, were adapted for the lens. Expression levels of both epithelial and fiber proteomes were compared with whole lens proteome and mRNA levels using E14.5, E16.5, E18.5, and P0.5 RNA-Seq data sets. During this developmental time window, multiple complex biosynthetic and catabolic processes generate the molecular and structural foundation for lens transparency. As expected, crystallins showed a high correlation between their mRNA and protein levels. Comprehensive data analysis confirmed and/or predicted roles for transcription factors (TFs), RNA-binding proteins (e.g. Carhsp1), translational apparatus including ribosomal heterogeneity and initiation factors, microtubules, cytoskeletal [e.g. non-muscle myosin IIA heavy chain (Myh9) and βB2-spectrin (Sptbn2)] and membrane proteins in lens formation and maturation. Our data highlighted many proteins with unknown functions in the lens that were preferentially enriched in epithelium or fibers, setting the stage for future studies to further dissect the roles of these proteins in fiber cell differentiation vs. epithelial cell maintenance. In conclusion, the present proteomic datasets represent the first mouse lens epithelium and fiber cell proteomes, establish comparative analyses of protein and RNA-Seq data, and characterize the major proteome remodeling required to form the mature lens fiber cells.

KW - Differentiation

KW - Lens

KW - Mass spectrometry

KW - Proteome

KW - RNA-Seq

KW - Transcription factors

KW - Transcriptome

UR - http://www.scopus.com/inward/record.url?scp=85055901225&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85055901225&partnerID=8YFLogxK

U2 - 10.1016/j.exer.2018.10.011

DO - 10.1016/j.exer.2018.10.011

M3 - Article

VL - 179

SP - 32

EP - 46

JO - Experimental Eye Research

T2 - Experimental Eye Research

JF - Experimental Eye Research

SN - 0014-4835

ER -