KTCNlncDB—a first platform to investigate lncRNAs expressed in human keratoconus and non-keratoconus corneas

Szcześniak, Michał Wojciech; Kabza, Michał; Karolak, Justyna A.; Rydzanicz, Małgorzata; Nowak, Dorota; Ginter-Matuszewska, Barbara; Polakowski, Piotr; Płoski, Rafał; Szaflik, Jacek P.; Gajęcka, Marzena

doi:10.1093/database/baw168

Cited by 14 publications

(12 citation statements)

References 34 publications

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“…These results have shown that some of those non-coding RNAs could affect the expression of at least 996 genes in keratoconus patients ( Table 1 ) (compared to healthy subjects). The differentially regulated genes include very relevant cellular metabolism and fate regulators such as TGF-β and SMAD9, SMAD6, TGFB3, and TGFBR1 members of Hippo/Wnt pathways ( Szczesniak et al, 2017 ). All those have been previously associated with keeping ocular health ( Morgan et al, 2013 ).…”

Section: Ocular Surface Disordersmentioning

confidence: 99%

Epigenetics in the Eye: An Overview of the Most Relevant Ocular Diseases

2017

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Sight for mammals is one of the most appreciated senses. In humans there are several factors that contribute to the increment in all kind of eye diseases. This mini-review will focus on some diseases whose prevalence is steadily increasing year after year for non-genetic reasons, namely cataracts, dry eye, and glaucoma. Aging, diet, inflammation, drugs, oxidative stress, seasonal and circadian style-of-live changes are impacting on disease prevalence by epigenetics factors, defined as stable heritable traits that are not explained by changes in DNA sequence. The mini-review will concisely show the data showing epigenetics marks in these diseases and on how knowledge on the epigenetic alterations may guide therapeutic approaches to have a healthy eye.

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Section: Ocular Surface Disordersmentioning

confidence: 99%

Epigenetics in the Eye: An Overview of the Most Relevant Ocular Diseases

2017

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“…By 2005, differentially expressed proteins in KC patients have been investigated using either the whole cornea, certain layer, or tears [19][20][21][22] . In 2017, Szcześniak et al and Kabza M et al used RNA-Seq to determine differentially expressed RNAs between KC-affected and other disease affected corneas 23 .…”

Section: Introductionmentioning

confidence: 99%

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

Khaled

Bykhovskaya

Yablonski

et al. 2018

Preprint

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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 2500Sequencer. 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. RESULTSUsing |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.

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“… 20 , 21 By 2005, differentially expressed proteins in KC patients have been investigated using the whole cornea, certain layer, or tears. 22 – 25 In 2017, Szcześniak et al 26 and Kabza et al 27 used RNA-Seq to determine differentially expressed RNAs between KC-affected and other disease affected corneas.…”

mentioning

confidence: 99%

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

Khaled

Bykhovskaya

Yablonski

et al. 2018

Invest. Ophthalmol. Vis. Sci.

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PurposeKeratoconus (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.MethodsFrom 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.ResultsUsing |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.ConclusionsOur RNA-Seq–based differential expression and correlation analyses have identified many potential KC contributing coding and noncoding RNAs.

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KTCNlncDB—a first platform to investigate lncRNAs expressed in human keratoconus and non-keratoconus corneas

Cited by 14 publications

References 34 publications

Epigenetics in the Eye: An Overview of the Most Relevant Ocular Diseases

Epigenetics in the Eye: An Overview of the Most Relevant Ocular Diseases

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

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

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