Proteome Landscape of Epithelial-to-Mesenchymal Transition (EMT) of Retinal Pigment Epithelium Shares Commonalities With Malignancy-Associated EMT

Autor: Karl J. Wahlin, Jun Wan, Ravi Chakra Turaga, Cynthia A. Berlinicke, Jiang Qian, Joseph L. Mertz, Melissa M. Liu, Ming-Wen Hu, Donald J. Zack, Srinivasa R. Sripathi, Julien Maruotti
Jazyk: angličtina
Rok vydání: 2021
Předmět:
retina
SLC
solute carrier
UR
upstream regulator
Proteome
Carcinogenesis
DIA
data-independent acquisition
Retinal Pigment Epithelium
Tandem mass tag
Proteomics
Biochemistry
Analytical Chemistry
Transcriptome
transcriptomics
Data-independent acquisition
AMD
age-related macular degeneration
Induced pluripotent stem cell
Cells
Cultured
EMT
PSM
peptide-spectrum match
Cell biology
ECM
extracellular matrix
medicine.anatomical_structure
embryonic structures
proteogenomics
RT
room temperature
hiPSC
human-induced pluripotent stem cell
FGFR
fibroblast growth factor receptor
RPE
retinal pigment epithelium
TEABC
triethylammonium bicarbonate
URA
upstream regulator analysis
Epithelial-Mesenchymal Transition
FDR
false discovery rate
Induced Pluripotent Stem Cells
hiPS/ES–RPE
hRPE
human stem cell–derived RPE
Biology
proteomics
STY
phosphoserine
threonine
and tyrosine
GO
Gene Ontology
medicine
Humans
Epithelial–mesenchymal transition
Molecular Biology
Embryonic Stem Cells
Retinal pigment epithelium
Research
TMT
tandem mass tag
MS
ACN
acetonitrile
bRPLC
basic reversed-phase LC
FC
fold change
IPA
ingenuity pathway analysis
STRING
Search Tool for the Retrieval of Interacting Genes/Proteins
eye diseases
Coculture Techniques
sense organs
qPCR
quantitative PCR
hESC
human-embryonic stem cell
EMT
epithelial-to-mesenchymal transition
Zdroj: Molecular & Cellular Proteomics : MCP
ISSN: 1535-9484
1535-9476
Popis: Stress and injury to the retinal pigment epithelium (RPE) often lead to dedifferentiation and epithelial-to-mesenchymal transition (EMT). These processes have been implicated in several retinal diseases, including proliferative vitreoretinopathy, diabetic retinopathy, and age-related macular degeneration. Despite the importance of RPE-EMT and the large body of data characterizing malignancy-related EMT, comprehensive proteomic studies to define the protein changes and pathways underlying RPE-EMT have not been reported. This study sought to investigate the temporal protein expression changes that occur in a human-induced pluripotent stem cell–based RPE-EMT model. We utilized multiplexed isobaric tandem mass tag labeling followed by high-resolution tandem MS for precise and in-depth quantification of the RPE-EMT proteome. We have identified and quantified 7937 protein groups in our tandem mass tag–based MS analysis. We observed a total of 532 proteins that are differentially regulated during RPE-EMT. Furthermore, we integrated our proteomic data with prior transcriptomic (RNA-Seq) data to provide additional insights into RPE-EMT mechanisms. To validate these results, we have performed a label-free single-shot data-independent acquisition MS study. Our integrated analysis indicates both the commonality and uniqueness of RPE-EMT compared with malignancy-associated EMT. Our comparative analysis also revealed that multiple age-related macular degeneration–associated risk factors are differentially regulated during RPE-EMT. Together, our integrated dataset provides a comprehensive RPE-EMT atlas and resource for understanding the molecular signaling events and associated biological pathways that underlie RPE-EMT onset. This resource has already facilitated the identification of chemical modulators that could inhibit RPE-EMT, and it will hopefully aid in ongoing efforts to develop EMT inhibition as an approach for the treatment of retinal disease.
Graphical Abstract
Highlights • Proteomics data were integrated with prior transcriptomic (RNA-Seq) data on RPE-EMT. • Dysregulated RPE-EMT proteome shares commonality with malignancy-associated EMT. • Altered RPE-EMT proteome signatures correlated with known AMD-associated risk factors. • Protein kinases and phosphatases crosstalk modulate RPE-EMT.
In Brief EMT can play a role in retinal diseases. Here, we present a comprehensive proteomic analysis aimed at defining the temporal protein expression changes associated with EMT of stem cell–derived retinal pigment epithelial cells. Tandem mass tag and direct data-independent acquisition MS approaches were performed after inducing RPE-EMT by enzymatic dissociation. We present integration of our proteomic data with prior transcriptomic (RNA-Seq) data to provide additional insights into the RPE-EMT progression.
Databáze: OpenAIRE
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