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Loretta Giummarra Vocale, Nina Riddell, Melanie J Murphy, Sheila Gillard Crewther; Commonalities between transcriptomic and proteomic profiles of FDM in chick. Invest. Ophthalmol. Vis. Sci. 2019;60(9):3150.
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© ARVO (1962-2015); The Authors (2016-present)
Form deprivation myopia (FDM) is associated with dramatic increases in ocular volume, axial length, and thinning of the retina and choroid. We have documented microarray and RNA-seq transcriptomic and label-free proteomic profiles in the chick FDM model, but have not yet analysed commonalities between these datasets. Thus this study aimed to identify and characterize gene and protein pathways consistently associated with FDM induction and recovery in our data.
Hatchling chicks were monocularly occluded from days 4-11, then given 0h, 6h or 24h of normal vision. Separate chicks were used as aged-matched unoccluded controls. For the transcriptome datasets, RNA was isolated from retina/RPE/choroid and prepared for Affymetrix microarray analysis or sequencing on the Illumina HiSeq 1500. For the proteomic dataset, retina/RPE/choroid was biopsied from the posterior eye cup and prepared for mass spectroscopy (MS). Following pre-processing, lists of differentially expressed (DE) genes and proteins generated by microarray, RNA-seq and MS were compared using the GeneOverlap R package, and p-values and odds ratios (ORs) were calculated for each intersection. Intersecting genes and proteins were then subject to gene ontology over-representation analysis using PANTHER.
DE proteins overlapped significantly with DE genes in the microarray (intersection=41,p<0.001, OR=2.93) and RNA-seq (intersection=18,p=0.006, OR=2.03) data. Concordance between the microarray and RNA-seq was also high, with 98 intersecting genes found (p<0.001, OR=3.23). Osteoglycin (OGN), Transgelin (TAGLN), and Tyrosinase-related protein 1 (TYRP1) were implicated across all three platforms. PANTHER analysis identified ‘visual perception’ (30.7 fold enrichment [FE], FDR<0.001) and ‘neurological system process’ (4.6 FE, FDR=0.003) as the most enriched biological processes in the list of intersecting genes and proteins. Genes implicated in both RNA-seq and microarray datasets were enriched for ‘circadian rhythm’ (43.2 FE, FDR<0.003), ‘angiogenesis’ (33.6 FE, FDR<0.004), and ‘visual perception’ (8.62 FE, FDR<0.023).
Our data indicates that abnormal axial growth during FD is accompanied by significant changes in retinal signal transduction at the mRNA and protein level. These results are consistent with our previous transcriptomic and proteomic work, highlighting the importance of these biological pathways in the myopic eye.
This abstract was presented at the 2019 ARVO Annual Meeting, held in Vancouver, Canada, April 28 - May 2, 2019.
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