June 2023
Volume 64, Issue 8
Open Access
ARVO Annual Meeting Abstract  |   June 2023
Identifying novel candidate coloboma genes through cross-species gene expression profiling
Author Affiliations & Notes
  • Daniel Sanchez-Mendoza
    OGVFB, National Eye Institute, Bethesda, Maryland, United States
  • Uma Neelathi
    OGVFB, National Eye Institute, Bethesda, Maryland, United States
  • David McGaughey
    OGVFB, National Eye Institute, Bethesda, Maryland, United States
  • Elangovan Boobalan
    OGVFB, National Eye Institute, Bethesda, Maryland, United States
  • Tiziana Cogliati
    National Institute on Aging, Bethesda, Maryland, United States
  • Brian Patrick Brooks
    OGVFB, National Eye Institute, Bethesda, Maryland, United States
  • Footnotes
    Commercial Relationships   Daniel Sanchez-Mendoza None; Uma Neelathi None; David McGaughey None; Elangovan Boobalan None; Tiziana Cogliati None; Brian Brooks None
  • Footnotes
    Support  none
Investigative Ophthalmology & Visual Science June 2023, Vol.64, 4763. doi:
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      Daniel Sanchez-Mendoza, Uma Neelathi, David McGaughey, Elangovan Boobalan, Tiziana Cogliati, Brian Patrick Brooks; Identifying novel candidate coloboma genes through cross-species gene expression profiling. Invest. Ophthalmol. Vis. Sci. 2023;64(8):4763.

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

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Abstract

Purpose : Uveal coloboma accounts for up to 10% of childhood blindness and is caused by incomplete closure of the optic fissure during early fetal eye development. Several genes are known to be important for the proper closure of the optic fissure; disruptions in these genes are predicted to cause coloboma. Therefore, identifying additional genes important in optic fissure closure (OFC) may lead to the identification of novel genes responsible for human coloboma.

Methods : We compiled the raw data and matched the expression profiles from four independent research articles: Brown et al. 2009, Cao et al. 2018, Patel et al. 2020, Richardson et al. 2019. Each of whom collected gene expression data from different model organisms: mice, zebrafish, humans. We were able to normalize the microarray expression data and RNAseq expression data for similar distribution to perform analysis across these different datasets. A time-course analysis comparing gene expression from before and during optic fissure fusion, as well as an analysis comparing the optic fissure to the optic cup during optic fissure fusion were analyzed and several potential coloboma candidate genes were identified. Further confirmation was performed through in situ hybridization on zebrafish for initial localization of expression, followed by morpholino knockdown injections in ABTL zebrafish to verify the viability of the gene candidates and any profound effects the genes may have on the eye.

Results : Candidate genes lum, trpm1, anxa3, dab1, wls, and apod were localized to the developing wild-type zebrafish eye by in situ hybridization during the time of OFC. Morpholino knockdowns of these genes are currently being conducted.

Conclusions : Our results are consistent with our hypothesis that cross-experiment analysis of gene expression data may help identify potential coloboma genes. These studies may improve our understanding of the molecular basis of OFC and assist in the identification of novel human disease genes.

This abstract was presented at the 2023 ARVO Annual Meeting, held in New Orleans, LA, April 23-27, 2023.

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