Next Generation Sequencing Analysis of Gene and Pathway Regulation in the Rat Model of Retinopathy of Prematurity

Abstract

Purpose: To identify the genes, biochemical signaling pathways, and biological themes involved in the pathogenesis of retinopathy of prematurity (ROP).

Methods: Next-generation sequencing was performed on the RNA transcriptome of rats with the Penn et al. (1994) oxygen-induced retinopathy model of ROP at the height of vascular abnormality, postnatal day 19, and normalized to age-matched, littermate controls. Custom developed pathways with potential relevance to known ROP sequellae were developed and evaluated for significant regulation in ROP. Regulation of other biological pathways and themes was detected by comparison with the online Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Database for Annotation, Visualization and Integrated Discovery (DAVID) genomic databases.

Results: In the custom pathway analyses, canonical Wnt signaling was found to be regulated, but the non-canonical PCP and Wnt/Ca²⁺ pathways were not. Nitric oxide (NO) signaling, as measured by the activation of nitric oxide synthase (NOS), neuronal (nNOS) and endothelial (eNOS), was also regulated, as was retinoic acid (RA) signaling. Biological themes related to protein translation (ribosomes), neural signaling, inflammation and immunity, cell cycle and cell death, were (among others) detected by KEGG and DAVID to be highly regulated in ROP rats.

Conclusions: ROP alters expression in many genes and pathways that may provide novel targets for intervention.

Keywords: 706 retinopathy of prematurity • 533 gene/expression • 688 retina