Dataset Information

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

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-?, 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.

SUBMITTER: Khaled ML

PROVIDER: S-EPMC5984031 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

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Publications

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

Khaled Mariam Lofty ML Bykhovskaya Yelena Y Yablonski Sarah E R SER Li Hanzhou H Drewry Michelle D MD Aboobakar Inas F IF Estes Amy A Gao X Raymond XR Stamer W Daniel WD Xu Hongyan H Allingham R Rand RR Hauser Michael A MA Rabinowitz Yaron S YS Liu Yutao Y

Investigative ophthalmology & visual science 20180601 7

<h4>Purpose</h4>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.<h4>Methods</h4>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 don ...[more]

PMID: 29860458

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Project description:Long non-coding (lnc)RNAs have been shown to have central roles in stress responses, cell identity and developmental processes in multicellular organisms as well as in unicellular fungi. Previous works have shown the occurrence of lncRNAs in diatoms, namely in Phaeodactylum tricornutum, many of which being expressed under specific stress conditions. Interestingly, P. tricornutum is the only known diatom that has a demonstrated morphological plasticity, occurring in three distinct morphotypes: fusiform, triradiate and oval. Although the morphotypes are interchangeable, the fusiform is the dominant one while both the triradiate and the oval forms are less common, the latter often being associated with stress conditions such as low salinity and solid culture media, amongst others. Nonetheless, the molecular basis underpinning morphotype identity in P. tricornutum remains elusive. Using twelve previously published transcriptomic datasets originating from the three morphotypes of P. tricornutum, we sought to investigate the expression patterns of lncRNAs (lincRNAs and NATs) in these distinct morphotypes, using pairwise comparisons, in order to explore the putative involvement of these noncoding molecules in morphotype identity. We found that differentially expressed lncRNAs cluster according to morphotype, indicating that lncRNAs are not randomly expressed, but rather seem to provide a specific (noncoding) transcriptomic signature of the morphotype. We also present evidence to suggest that the major differences in DE genes (both noncoding and coding) between the stress related oval morphotype and the most common fusiform morphotype could be due, to a large extent, to the hyposaline culture conditions rather than to the morphotype itself. However, several lncRNAs associated to each one of the three morphotypes were identified, which could have a potential role in morphotype (or cell) identity in P. tricornutum, similar to what has been found in both animals and plant development.

Dataset Information

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

Publications

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

Similar Datasets

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