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

Publication ,  Journal Article
Khaled, ML; Bykhovskaya, Y; Yablonski, SER; Li, H; Drewry, MD; Aboobakar, IF; Estes, A; Gao, XR; Stamer, WD; Xu, H; Allingham, RR; Hauser, MA ...
Published in: Invest Ophthalmol Vis Sci
June 1, 2018

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: 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. 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 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. CONCLUSIONS: Our RNA-Seq-based differential expression and correlation analyses have identified many potential KC contributing coding and noncoding RNAs.

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Published In

Invest Ophthalmol Vis Sci

DOI

EISSN

1552-5783

Publication Date

June 1, 2018

Volume

59

Issue

7

Start / End Page

2717 / 2728

Location

United States

Related Subject Headings

  • Young Adult
  • Sequence Analysis, RNA
  • RNA, Messenger
  • RNA, Long Noncoding
  • Polymerase Chain Reaction
  • Ophthalmology & Optometry
  • Middle Aged
  • Male
  • Keratoconus
  • Humans
 

Citation

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Khaled, M. L., Bykhovskaya, Y., Yablonski, S. E. R., Li, H., Drewry, M. D., Aboobakar, I. F., … Liu, Y. (2018). Differential Expression of Coding and Long Noncoding RNAs in Keratoconus-Affected Corneas. Invest Ophthalmol Vis Sci, 59(7), 2717–2728. https://doi.org/10.1167/iovs.18-24267
Khaled, Mariam Lofty, Yelena Bykhovskaya, Sarah E. R. Yablonski, Hanzhou Li, Michelle D. Drewry, Inas F. Aboobakar, Amy Estes, et al. “Differential Expression of Coding and Long Noncoding RNAs in Keratoconus-Affected Corneas.Invest Ophthalmol Vis Sci 59, no. 7 (June 1, 2018): 2717–28. https://doi.org/10.1167/iovs.18-24267.
Khaled ML, Bykhovskaya Y, Yablonski SER, Li H, Drewry MD, Aboobakar IF, et al. Differential Expression of Coding and Long Noncoding RNAs in Keratoconus-Affected Corneas. Invest Ophthalmol Vis Sci. 2018 Jun 1;59(7):2717–28.
Khaled, Mariam Lofty, et al. “Differential Expression of Coding and Long Noncoding RNAs in Keratoconus-Affected Corneas.Invest Ophthalmol Vis Sci, vol. 59, no. 7, June 2018, pp. 2717–28. Pubmed, doi:10.1167/iovs.18-24267.
Khaled ML, Bykhovskaya Y, Yablonski SER, Li H, Drewry MD, Aboobakar IF, Estes A, Gao XR, Stamer WD, Xu H, Allingham RR, Hauser MA, Rabinowitz YS, Liu Y. Differential Expression of Coding and Long Noncoding RNAs in Keratoconus-Affected Corneas. Invest Ophthalmol Vis Sci. 2018 Jun 1;59(7):2717–2728.

Published In

Invest Ophthalmol Vis Sci

DOI

EISSN

1552-5783

Publication Date

June 1, 2018

Volume

59

Issue

7

Start / End Page

2717 / 2728

Location

United States

Related Subject Headings

  • Young Adult
  • Sequence Analysis, RNA
  • RNA, Messenger
  • RNA, Long Noncoding
  • Polymerase Chain Reaction
  • Ophthalmology & Optometry
  • Middle Aged
  • Male
  • Keratoconus
  • Humans