Differential expression of coding and long noncoding rnas in keratoconus-affected corneas

Mariam Lofty Khaled, Yelena Bykhovskaya, Sarah E.R. Yablonski, Hanzhou Li, Michelle D. Drewry, Inas F. Aboobakar, Amy Johnston Estes, X. Raymond Gao, W. Daniel Stamer, Hongyan Xu, R. Rand Allingham, Michael A. Hauser, Yaron S. Rabinowitz, Yutao Liu

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)2717-2728
Number of pages12
JournalInvestigative Ophthalmology and Visual Science
Volume59
Issue number7
DOIs
StatePublished - Jun 2018

Fingerprint

Long Noncoding RNA
Keratoconus
Cornea
RNA
Cell Movement
Untranslated RNA
Genes
Pathologic Dilatations
Ribosomal RNA
Extracellular Matrix Proteins
Extracellular Space
Glycosaminoglycans
Phosphatidylinositol 3-Kinases
Protein Binding
Cell Adhesion
Cytokines

Keywords

  • Coding RNAs
  • Cornea
  • Keratoconus
  • LncRNAs
  • RNA-seq

ASJC Scopus subject areas

  • Ophthalmology
  • Sensory Systems
  • Cellular and Molecular Neuroscience

Cite this

Differential expression of coding and long noncoding rnas in keratoconus-affected corneas. / Khaled, Mariam Lofty; Bykhovskaya, Yelena; Yablonski, Sarah E.R.; Li, Hanzhou; Drewry, Michelle D.; Aboobakar, Inas F.; Estes, Amy Johnston; Gao, X. Raymond; Stamer, W. Daniel; Xu, Hongyan; Allingham, R. Rand; Hauser, Michael A.; Rabinowitz, Yaron S.; Liu, Yutao.

In: Investigative Ophthalmology and Visual Science, Vol. 59, No. 7, 06.2018, p. 2717-2728.

Research output: Contribution to journalArticle

Khaled, ML, Bykhovskaya, Y, Yablonski, SER, Li, H, Drewry, MD, Aboobakar, IF, Estes, AJ, Gao, XR, Stamer, WD, Xu, H, Allingham, RR, Hauser, MA, Rabinowitz, YS & Liu, Y 2018, 'Differential expression of coding and long noncoding rnas in keratoconus-affected corneas', Investigative Ophthalmology and Visual Science, vol. 59, no. 7, pp. 2717-2728. https://doi.org/10.1167/iovs.18-24267
Khaled, Mariam Lofty ; Bykhovskaya, Yelena ; Yablonski, Sarah E.R. ; Li, Hanzhou ; Drewry, Michelle D. ; Aboobakar, Inas F. ; Estes, Amy Johnston ; Gao, X. Raymond ; Stamer, W. Daniel ; Xu, Hongyan ; Allingham, R. Rand ; Hauser, Michael A. ; Rabinowitz, Yaron S. ; Liu, Yutao. / Differential expression of coding and long noncoding rnas in keratoconus-affected corneas. In: Investigative Ophthalmology and Visual Science. 2018 ; Vol. 59, No. 7. pp. 2717-2728.
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abstract = "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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T1 - Differential expression of coding and long noncoding rnas in keratoconus-affected corneas

AU - Khaled, Mariam Lofty

AU - Bykhovskaya, Yelena

AU - Yablonski, Sarah E.R.

AU - Li, Hanzhou

AU - Drewry, Michelle D.

AU - Aboobakar, Inas F.

AU - Estes, Amy Johnston

AU - Gao, X. Raymond

AU - Stamer, W. Daniel

AU - Xu, Hongyan

AU - Allingham, R. Rand

AU - Hauser, Michael A.

AU - Rabinowitz, Yaron S.

AU - Liu, Yutao

PY - 2018/6

Y1 - 2018/6

N2 - 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.

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. 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.

KW - Coding RNAs

KW - Cornea

KW - Keratoconus

KW - LncRNAs

KW - RNA-seq

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