Regional transcriptome map of the adult rhesus macaque retina and RPE-choroid

Abstract

Purpose : Molecular determinants of specialized human ocular tissues remain unclear, as few species possess a human-like fovea. We sought to create a macaque foveal transcriptional profile to further understand conserved elements of higher acuity vision. We performed transcriptomic sequencing across the macular/foveal, perimacular, and peripheral regions of the neural retina and retinal pigment epithelium (RPE)-choroid tissues in adult macaques to characterize region- and tissue-specific gene expression.

Methods : Four eyes were obtained from two adult rhesus monkeys (Macaca mulatta). Two mm punch biopsies were removed from the three regions of each eye. After dissecting the retina and RPE-choroid tissue, RNA was isolated for gene expression profiling by RNA-seq. Raw RNA-seq data was analyzed using Salmon pseudo-alignment transcript quantification tool. Expression patterns were analyzed via gene expression clustering, gene ontology (GO) term enrichment analysis, and pathway analysis tools.

Results : Differential comparison between tissues and across regions indicated that the retina and RPE-choroid have distinct molecular profiles in each region as revealed by principal component analysis and clustering. Comparison of the fovea and peripheral regions in both tissues indicated pronounced differential gene expression with 9644 and 7925 differentially expressed genes in retina and RPE/choroid, respectively. In contrast, in fovea vs perimacular comparisons, the retina showed 4633 genes and RPE/choroid showed only 414 genes with different expression. Top foveal retina enrichment included actin and RNA binding pathways, and foveal RPE/choroid was enriched for cadherin and RNA binding pathway genes.

Conclusions : Using high throughput comparative transcriptomic analysis, we defined foveal gene enrichment in a non-human primate model. Regional differential expression in the macaque was greater than that found in previously published transcriptome analysis of the human retina and RPE/choroid. Further analysis across regions and between tissues in addition to comparison to human data will help identify conserved fovea-enriched genes. Specific pathways identified through GO enrichment analysis will provide insight into the role of these differentially expressed genes in development.

This abstract was presented at the 2019 ARVO Annual Meeting, held in Vancouver, Canada, April 28 - May 2, 2019.