September 2016
Volume 57, Issue 12
Open Access
ARVO Annual Meeting Abstract  |   September 2016
Differential gene expression and pathway enrichment in the human cornea and retina
Author Affiliations & Notes
  • Xiaoyi (Raymond) Gao
    Ophthalmology, University of Illinois, Chicago, Illinois, United States
  • Drew Nannini
    Ophthalmology, University of Illinois, Chicago, Illinois, United States
  • Kristen Goulee
    Ophthalmology, University of Illinois, Chicago, Illinois, United States
  • Inas F Aboobakar
    Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
  • R Rand Allingham
    Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
  • Michael A Hauser
    Medicine and Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
  • Yutao Liu
    Cellular Biology and Anatomy, Medical College of Georgia, Augusta, Georgia, United States
  • Footnotes
    Commercial Relationships   Xiaoyi (Raymond) Gao, None; Drew Nannini, None; Kristen Goulee, None; Inas Aboobakar, None; R Rand Allingham, None; Michael Hauser, None; Yutao Liu, None
  • Footnotes
    Support  NIH Grant R01EY022651, Departmental Core Grant P30EY001792, Midwest Eye-Banks
Investigative Ophthalmology & Visual Science September 2016, Vol.57, 6567. doi:
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      Xiaoyi (Raymond) Gao, Drew Nannini, Kristen Goulee, Inas F Aboobakar, R Rand Allingham, Michael A Hauser, Yutao Liu; Differential gene expression and pathway enrichment in the human cornea and retina. Invest. Ophthalmol. Vis. Sci. 2016;57(12):6567.

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

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Abstract

Purpose : The cornea and the retina are major contributors to normal vision in the human eye. The cornea is a highly organized structure of proteins and cells designed to focus light coming into the eye on the retina and as an important component of the globe, protects the eye from environmental injury and infection. The retina is composed of neuronal photoreceptor cells, which convert light into recognizable neural signals sent to the brain. There is an unmet need to understand the genetic basis for the functional differences between the cornea and the retina. We used RNA-Seq to identify gene signatures attributing to the functional differences between these two tissues.

Methods : We performed RNA-Seq analysis on seven normal human corneas and three normal human retinas obtained from adult postmortem subjects. All the RNA-Seq data were strand-specific and paired-end obtained from the Illumina HiSeq instruments. RNA-Seq reads alignment was performed using TopHat and differentially expressed genes were identified by Cuffdiff. IPA and WebGestalt were used for functional enrichment analyses.

Results : Genes expressed significantly higher in the cornea than in the retina were involved in pathways associated with protein synthesis, cellular turnover, and cellular defenses, such as EIF2 signaling, eIF4 and p70S6K signaling, mTOR signaling, apoptosis, and leukocyte extravasation. These genes are enriched in epidermal thickening and sparse hair related phenotypes and carcinomas. Conversely, genes expressed more highly in the retina than in the cornea were involved in pathways associated with blood vessels and phototransduction, such as cellular effects of sildenafil, beta-adrenergic signaling, PKA signaling, phototransduction, and glutamate signaling. These genes are enriched in photoreception related phenotypes and nervous system diseases.

Conclusions : Using high-throughput RNA-Seq, we identified distinct gene expression signatures in normal human cornea and retina tissues that can serve as reference gene sets for the investigation of the physiology and pathology of these tissues. To our knowledge, we are the first to report pathway enrichment specific to the cornea and the retina. In addition, to expand our current knowledge of the genetic basis of the cornea and the retina, this study highlights that we can use normal eye tissues to prioritize key ocular genes and pathways, which may cause ocular diseases if disrupted.

This is an abstract that was submitted for the 2016 ARVO Annual Meeting, held in Seattle, Wash., May 1-5, 2016.

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