Omics analyses in keratoconus: from transcriptomics to proteomics.

Abstract

To summarize the recent advances in transcriptomics and proteomics studies of keratoconus using advanced genome-wide gene and protein expression profiling techniques. Second-generation sequencing including RNA sequencing has been widely used to characterize the genome-wide gene expression in corneal tissues or cells affected by keratoconus. Due to different sample types, sequencing platforms, and analysis pipeline, 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. 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, up-to-date platform and bioinformatics tools.