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Identification of Key Genes and Pathways in Persistent Hyperplastic Primary Vitreous of the Eye Using Bioinformatic
Derin M Thomas1, Chitra Kannabiran1, D Balasubramanian1
1Kallam Anji Reddy Molecular Genetics Laboratory, Prof. Brien Holden Eye Research Center, LV Prasad Eye Institute, Hyderabad, India.
Frontiers in Medicine
|September 6, 2021
Summary
This study identifies 14 key genes and 4 major pathways involved in persistent hyperplastic primary vitreous (PHPV), a congenital eye disease. It also reveals 26 FDA-approved drugs as potential treatments for PHPV.
Area of Science:
- Ophthalmology and Genetics
- Bioinformatics and Computational Biology
- Developmental Biology
Background:
- Persistent hyperplastic primary vitreous (PHPV) is a congenital eye disease caused by the failure of the embryonic hyaloid vascular system to regress.
- The molecular mechanisms, candidate genes, and therapeutic targets for PHPV remain largely unknown.
- This study aims to elucidate the genetic and molecular underpinnings of PHPV using comprehensive bioinformatics analysis.
Purpose of the Study:
- To identify key genes and molecular pathways associated with persistent hyperplastic primary vitreous (PHPV).
- To evaluate potential therapeutic agents for the management of PHPV.
- To provide a foundation for novel targeted therapies for PHPV.
Main Methods:
- Text mining using pubmed2ensembl to identify PHPV-associated genes.
- Gene functional enrichment analysis using GeneCodis, DAVID, ClueGO, and CluePedia for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways.
- Protein-protein interaction (PPI) network construction and module analysis using STRING and Cytoscape, followed by drug-gene interaction analysis with DGIdb.
Main Results:
- Identified 50 genes associated with PHPV, revealing 35 enriched GO terms and 15 KEGG pathways.
- Constructed a PPI network, identifying 14 hub genes including TP53, VEGFA, SMAD2, and PAX6, primarily involved in eye morphogenesis and signaling pathways.
- Discovered 26 FDA-approved drugs targeting 7 of the 14 hub genes, indicating potential therapeutic candidates for PHPV.
Conclusions:
- The study identified 14 potential core genes and 4 major molecular pathways implicated in PHPV.
- A significant finding is the identification of 26 existing drugs that could be repurposed for PHPV treatment.
- These findings offer a basis for developing novel targeted therapies for persistent hyperplastic primary vitreous.
