July 2019
Volume 60, Issue 9
Open Access
ARVO Annual Meeting Abstract  |   July 2019
Transcriptome of the canine macular RPE/choroid and retina: parallels with human macular gene expression
Author Affiliations & Notes
  • Freya Mowat
    Clinical Sciences, North Carolina State University, Raleigh, North Carolina, United States
  • Melanie Foster
    Clinical Sciences, North Carolina State University, Raleigh, North Carolina, United States
  • Dereje Jima
    Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, United States
    Bioinformatics Research Center, College of Sciences, North Carolina State University, Raleigh, North Carolina, United States
  • Footnotes
    Commercial Relationships   Freya Mowat, None; Melanie Foster, None; Dereje Jima, None
  • Footnotes
    Support  NIEHS P30ES025128
Investigative Ophthalmology & Visual Science July 2019, Vol.60, 6053. doi:
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      Freya Mowat, Melanie Foster, Dereje Jima; Transcriptome of the canine macular RPE/choroid and retina: parallels with human macular gene expression. Invest. Ophthalmol. Vis. Sci. 2019;60(9):6053.

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      © ARVO (1962-2015); The Authors (2016-present)

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Abstract

Purpose : The human macular retina and RPE/choroid/sclera have unique gene expression signatures, with 2051 and 926 differentially expressed genes respectively, compared with the retinal periphery. We have demonstrated that the dog retina also possesses a macular region of cone enrichment, and RPE morphologic differences between macula and periphery. We tested the hypothesis that gene expression of canine retina and RPE/choroid would differ between macula and periphery using RNASeq of post-mortem canine tissues.

Methods : We generated Illumina directional libraries and performed RNA sequencing (Illumina HiSeq 2500, 125bp SE) on tissues from 4 mixed breed canine eyes (2 female, 2 male). Mean RNA integrity number was 9.35 ± 0.18, mean read depth was 33.6 ± 1.0 million reads/sample. Sequence quality was assessed using FastQC and the first 10 bases with poor quality were trimmed from the 5’-end. The remaining reads were aligned with STAR aligner to the reference CanFam3.1 genome. The number of reads mapped to a Dog genome features ware determined using htseq-count script from HTSeq python package and the count data was imported to R statistical computing environment for further analysis. Differentially expressed (DE) genes were identified using DESeq2 (adjusted for multiple correction using Benjamini-Hochberg procedure); further analysis was performed on genes which had >2 fold change of difference and an adjusted P value of P <0.05. Ingenuity Pathway Analysis (Qiagen) was used to identify gene pathways in differentially expressed gene sets.

Results : Differential expression between tissues (retina vs. RPE/choroid) was larger than between different locations within the same tissue. There were 918 DE genes between macular and peripheral retina (679 higher, 239 lower in the macula), and 2150 DE genes between macular and peripheral RPE/choroid (1123 higher, 1027 lower in the macula). Highly expressed macular pathways included those involved in retinal calcium signaling (z-score 3.4), and RPE/choroid ephrin receptor signaling (z-score 2.3).

Conclusions : These data further substantiate the similarities between dog and human central retina, and provide additional support for the use of dogs as models for heritable and complex macular disorders in humans.

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

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