RT Journal Article
SR Electronic
T1 Differential Expression of Coding and Long Noncoding RNAs in Keratoconus-affected Corneas
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 267054
DO 10.1101/267054
A1 Mariam Lofty Khaled
A1 Yelena Bykhovskaya
A1 Sarah E.R. Yablonski
A1 Hanzhou Li
A1 Michelle D. Drewry
A1 Inas F. Aboobakar
A1 Amy Estes
A1 Xiaoyi Gao
A1 W. Daniel Stamer
A1 Hongyan Xu
A1 R. Rand Allingham
A1 Michael A. Hauser
A1 Yaron S. Rabinowitz
A1 Yutao Liu
YR 2018
UL http://biorxiv.org/content/early/2018/02/18/267054.abstract
AB PURPOSE 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.METHODS 200ng total RNA from the corneas of 10 KC patients and 8 non-KC normal controls was used to prepare sequencing libraries with the SMARTer Stranded RNA-Seq kit after ribosomal RNA depletion. Paired-end 50bp sequences were generated using Illumina HiSeq 2500 Sequencer. Differential analysis was done using TopHat and 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.RESULTS 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 with cell migration/motility, extracellular space, cytokine response, and cell adhesion, suggesting the potential functions of these correlated lncRNAs, especially those with multiple pairs of correlations.CONCLUSIONS Our RNA-Seq based differential expression and correlation analyses have identified many potential KC contributing coding and noncoding RNAs.