Differential Expression of Coding and Long Noncoding RNAs in Keratoconus-Affected Corneas.

Abstract

Keratoconus (KC) is the most common corneal ectasia. We aimed to determine the differential expression of coding and long noncoding RNAs (lncRNAs) in human corneas affected with KC.From the corneas of 10 KC patients and 8 non-KC healthy controls, 200 ng total RNA was used to prepare sequencing libraries with the SMARTer Stranded RNA-Seq kit after ribosomal RNA depletion, followed by paired-end 50-bp sequencing with Illumina Sequencer. Differential analysis was done using TopHat/Cufflinks with a gene file from Ensembl and a lncRNA file from NONCODE. Pathway analysis was performed using WebGestalt. Using the expression level of differentially expressed coding and noncoding RNAs in each sample, we correlated their expression levels in KC and controls separately and identified significantly different correlations in KC against controls followed by visualization using Cytoscape.Using |fold change| ≥ 2 and a false discovery rate ≤ 0.05, we identified 436 coding RNAs and 584 lncRNAs with differential expression in the KC-affected corneas. Pathway analysis indicated the enrichment of genes involved in extracellular matrix, protein binding, glycosaminoglycan binding, and cell migration. Our correlation analysis identified 296 pairs of significant KC-specific correlations containing 117 coding genes enriched in functions related to cell migration/motility, extracellular space, cytokine response, and cell adhesion. Our study highlighted the potential roles of several genes (CTGF, SFRP1, AQP5, lnc-WNT4-2:1, and lnc-ALDH3A2-2:1) and pathways (TGF-β, WNT signaling, and PI3K/AKT pathways) in KC pathogenesis.Our RNA-Seq-based differential expression and correlation analyses have identified many potential KC contributing coding and noncoding RNAs.

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Citation

Published Version (Please cite this version)

10.1167/iovs.18-24267

Publication Info

Khaled, Mariam Lofty, Yelena Bykhovskaya, Sarah ER Yablonski, Hanzhou Li, Michelle D Drewry, Inas F Aboobakar, Amy Estes, X Raymond Gao, et al. (2018). Differential Expression of Coding and Long Noncoding RNAs in Keratoconus-Affected Corneas. Investigative ophthalmology & visual science, 59(7). pp. 2717–2728. 10.1167/iovs.18-24267 Retrieved from https://hdl.handle.net/10161/17225.

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Scholars@Duke

Stamer

W Daniel Stamer

Joseph A.C. Wadsworth Distinguished Professor of Ophthalmology

My laboratory studies the disease of glaucoma, the second leading cause of blindness in the United States, affecting nearly 3 million people (70 million Worldwide). The primary risk factor for developing glaucoma is ocular hypertension (high intraocular pressure, IOP). IOP is a function of the regulated movement of aqueous humor into and out of the eye.  Elevated IOP in glaucoma is a result of disease in the primary efflux route, the conventional outflow pathway, affecting proper homeostatic control of aqueous humor drainage.

Lowering IOP in glaucoma patients, whether or not they have ocular hypertension, is important because large clinical trials involving tens of thousands of patients repeatedly demonstrate that significant, sustained IOP reduction slows or halts vision loss. Unfortunately, current first-line medical treatments do not target the diseased conventional pathway and do not lower IOP sufficiently in most people with glaucoma. Therefore, finding new, more effective ways to medically control IOP by targeting the conventional pathway is a central goal the Stamer Laboratory.

Using molecular, cellular, organ and mouse model systems, my laboratory seeks to identify and validate novel drug targets in the human conventional outflow pathway to facilitate the development of the next generation of treatments for ocular hypertension and glaucoma.

Hauser

Michael Arthur Hauser

Professor in Medicine

Dr. Hauser has a strong interest in ocular genetics. Genomic studies at the Center for Human Genetics have identified multiple linkage peaks and susceptibility genes in primary open angle glaucoma (POAG) and age related macular degeneration (AMD). Dr. Hauser has recently accepted a 20% appointment at the Singapore Eye Research INstitute and the Duke/National University of Singapore.  In collaboration with multiple collaborators in Singapore, and Dr. Rand Allingham at the Duke Eye Center, Dr. Hauser is currently conducting a genome wide association study for glaucoma in individuals of African ancestry. These investigations include large datasets collected in Ghana, Nigeria, and South Africa.  
 
Dr. Hauser is also involved in collaborative investigations into the genetics of post-tramatic stress disorder in US veterans from Iraq and Afghanistan.   Major collaborators include Dr. Allison Ashley Koch, Dr. Jean Beckham, Dr. Christine Marx and the MIRECC Collaborative group at the Durham Veteran's Administration.  We have published a genome wide association study, as well as numerous investigations into candidate genes.  Epigenomic DNA methylation analysis and gene expression analysis of 3500 individuals is currently ongoing. 


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