Omics Analyses in Keratoconus: from Transcriptomics to Proteomics
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CORNEA
Omics Analyses in Keratoconus: from Transcriptomics to Proteomics Jingwen Cai 1 & Amy Estes 2,3 & Yutao Liu 1,3,4
# Springer Science+Business Media, LLC, part of Springer Nature 2020
Abstract Purpose of Review To summarize the recent advances in transcriptomics and proteomics studies of keratoconus using advanced genome-wide gene and protein expression profiling techniques. Recent Findings Second-generation sequencing including RNA sequencing has been widely used to characterize the genomewide gene expression in corneal tissues or cells affected by keratoconus (KC). Due to variations in sample types, sequencing platforms, and analysis pipelines, different lists of genes have been identified to be differentially expressed in KC-affected samples. Gene ontology and pathway/network analyses have indicated the involvement of genes related with extracellular matrix, WNT signaling, TGFβ pathway, and NRF2-regulated network. High-throughput proteomics studies using mass spectrometry have uncovered many KC-related protein molecules in pathways related with cytoskeleton, cell matrix, TGFβ signaling, and extracellular matrix remodeling, consistent with gene expression profiling. Summary Both transcriptomics and proteomics studies using genome-wide gene/protein expression profiling techniques have identified significant genes/proteins that may contribute to the pathogenesis of keratoconus. These molecules may be involved in functional categories related with extracellular matrix and TGFβ signaling. It is necessary to perform comprehensive gene/protein expression studies using larger sample size, same type of samples, and up-to-date platform and bioinformatics tools. Keywords Cornea . Keratoconus . Genetics . Transcriptomics . Proteomics
Introduction Keratoconus (KC) is one of the leading causes of corneal transplantation worldwide. In recent years, the advances in KC diagnosis and management have improved the quality of This article is part of the Topical Collection on Cornea * Yutao Liu [email protected]
vision in patients and attracted scientific research interest in the disorder. However, the etiology and pathogenesis of KC remain unclear. KC is a complex disorder with the involvement of both genetic and environmental risk factors [21, 51, 72], calling for novel approaches to study underlying mechanisms of this multifactorial disease [18, 75]. The advent of high-throughput technologies in transcriptomics and proteomics provides the opportunity to collect global information from invaluable patients’ samples and then analyze their dynamic responses in the disease condition [33, 50].
Jingwen Cai [email protected] Amy Estes [email protected]
Keratoconus
1
Department of Cellular Biology and Anatomy, Augusta University, 1460 Laney Walker Blvd, CB1101, Augusta, GA 30912, USA
2
Department of Ophthalmology, Augusta University, Augusta, GA 30912, USA
3
James & Jean Culver Vision Discovery Institute, Augusta University, Augusta, GA 30912, USA
4
Center for Biotechnology and Genomic Medicine, Augusta University,
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