Transcriptional Profile and Integrative Analyses of Long Noncoding RNAs in Primary Human Corneal Epithelial Cells in Response to HSV-1 Infection

ABSTRACT

Purpose

Long noncoding RNAs (lncRNAs) have been demonstrated to have important regulatory functions in diverse cellular processes; however, the role of lncRNAs in the pathogenesis of herpes simplex keratitis (HSK) remains poorly understood.

Methods

Primary human corneal epithelial cells (HCECs) were infected with herpes simplex virus-1 (HSV-1) and the total RNAs extracted from both the infected group and the mock-infected group subjected to microarray analysis to identify the differential expression of lncRNAs and mRNAs. We also performed bioinformatic analysis including gene ontology (GO) analysis, pathway analysis and co-expression network analysis.

Results

Compared with mock-infected group, the expression of thousands of lncRNAs and mRNAs were significantly changed, and the microarray results were validated by qRT-PCR. The most enriched GOs targeted by up-regulated transcripts were defense response, intrinsic component of plasma membrane and cytokine activity，and the most enriched GOs targeted by the down-regulated transcripts were cellular metabolic process, intracellular part and poly (A) RNA binding. Pathway analysis indicated that the most correlated pathways for up- and down-regulated transcripts were cytokine-cytokine receptor interaction and RNA transport, respectively.

Conclusions

Our study identified the genome-wide profile of lncRNAs and mRNAs expression in primary corneal epithelial cells with HSV-1 infection. These transcriptomic data together with subsequent bioinformatic analysis will provide us with novel clue to the insight into molecular mechanism and potential therapeutic targets of HSK. Further studies are expected to verify the potentially functional genes and pathways and explore the critical lncRNAs.

Abbreviations

Long noncoding RNAs: lncRNAs; herpes simplex virus-1: HSV-1; herpes simplex virus keratitis: HSK; human corneal epithelial cells: HCECs

KEYWORDS:

• Long noncoding RNAs
• cornea
• epithelial cells
• HSV-1
• viral infection

Acknowledgments

None.

Declaration of Interests

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.

Supplementary material

Supplemental data for this article can be access on the publisher’s website.

Additional information

Funding

This study is supported by the National Natural Science Foundation of China (81770897, 81570814, 81300271), Natural Science Foundation of Guangdong Province, China (2014A030313363, 2017A030313582, 2017A030313544) and Scientific Research project of Guangzhou Municipal Education Department (1201410345; Guangzhou City, Guangdong Province, China)