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| Status |
Public on Jul 28, 2016 |
| Title |
Human Corneal microRNA Expression Profile in Fungal Keratitis |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
MicroRNAs (miRNAs) are small, stable non-coding RNA molecules with regulatory function and marked tissue specificity that post-transcriptionally regulate gene expression, however their role in fungal keratitis remain unknown. Our purpose was to identify the miRNAs in human cornea from fungal keratitis patients and understand their key role in regulation of pathogenesis. Corneal samples from normal cadaver (n=3) and fungal keratitis (n=5) patients were pooled separately and total RNA was extracted. Deep sequencing was done using Illumina HiSeq1000 platform to identify miRNA profile. We identified seventy five differentially expressed miRNAs in fungal keratitis corneas. Select miRNAs were validated by real-time RT-PCR (Q-PCR). We predicted their role in regulating target genes in several pathways by combining miRNA target genes and pathway analysis, and mRNA expression of select target genes were further analysed by Q-PCR. MiR-21-5p, miR-223-3p, miR-146b-5p, miR-155-5p, miR-511-5p were found to be involved in inflammatory and immune responses, regulating Toll like receptor signaling pathways, which is of particular interest. MiR-451a with an increased expression in keratitis may have a role in wound healing by targeting Macrophage Migration Inhibitory Factor (MIF). Further, we highlighted that Neurotrophin signaling pathway may play a role in wound healing process. One novel miRNA was also detected in cornea. In conclusion, several miRNAs with high expression in fungal keratitis corneas point towards their role in regulation of pathogenesis. Further insights in understanding miRNAs role in wound healing and inflammation may help design new therapeutic strategies.
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| Overall design |
Control and fungal keratitis, human corneal miRNA profiles were generated using IlluminaHiseq1000 platform
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| Contributor(s) |
Devarajan B, Prajna L |
| Citation(s) |
26720440 |
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| Submission date |
Jan 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Bharanidharan Devarajan |
| E-mail(s) |
bharanid@gmail.com
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| Organization name |
Aravind Medical Research Foundation
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| Department |
Bioinformatics
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| Street address |
1,Anna nagar
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| City |
Madurai |
| State/province |
Tamil Nadu |
| ZIP/Postal code |
625020 |
| Country |
India |
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| Platforms (1) |
| GPL15433 |
Illumina HiSeq 1000 (Homo sapiens) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA272148 |
| SRA |
SRP051979 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE64843_RAW.tar |
60.0 Kb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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