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MicroRNA Expression Profiles of Human iPS Cells, Retinal Pigment Epithelium Derived From iPS, and Fetal Retinal Pigment Epithelium
Published on: June 24, 2014
MicroRNA profiling in intraocular medulloepitheliomas
Deepak P Edward1, Hind Alkatan2, Qundeel Rafiq3
1King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia; Wilmer Eye Institute, John Hopkins University School Of Medicine, Baltimore, MD, United States of America.
Purpose:
To study the differential expression of microRNA (miRNA) profiles between intraocular medulloepithelioma (ME) and normal control tissue (CT).
Material And Methods:
Total RNA was extracted from formalin fixed paraffin embedded (FFPE) intraocular ME (n=7) and from age matched ciliary body controls (n=8). The clinical history and phenotype was recorded. MiRNA profiles were determined using the Affymetrix GeneChip miRNA Arrays analyzed using expression console 1.3 software. Validation of significantly dysregulated miRNA was confirmed by quantitative real-time PCR. The web-based DNA Intelligent Analysis (DIANA)-miRPath v2.0 was used to perform enrichment analysis of differentially expressed (DE) miRNA gene targets in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway.
Results:
The pathologic evaluation revealed one benign (benign non-teratoid, n=1) and six malignant tumors (malignant teratoid, n=2; malignant non-teratoid, n = 4). A total of 88 miRNAs were upregulated and 43 miRNAs were downregulated significantly (P<0.05) in the tumor specimens. Many of these significantly dysregulated miRNAs were known to play various roles in carcinogenesis and tumor behavior. RT-PCR validated three significantly upregulated miRNAs and three significantly downregulated miRNAs namely miR-217, miR-216a, miR-216b, miR-146a, miR-509-3p and miR-211. Many DE miRNAs that were significant in ME tumors showed dysregulation in retinoblastoma, glioblastoma, and precursor, normal and reactive human cartilage. Enriched pathway analysis suggested a significant association of upregulated miRNAs with 15 pathways involved in prion disease and several types of cancer. The pathways involving significantly downregulated miRNAs included the toll-like receptor (TLR) (p<4.36E-16) and Nuclear Factor kappa B (NF-κB) signaling pathways (p<9.00E-06).
Conclusions:
We report significantly dysregulated miRNAs in intraocular ME tumors, which exhibited abnormal profiles in other cancers as well such as retinoblastoma and glioblastoma. Pathway analysis of all dysregulated miRNAs shared commonalities with other cancer pathways.
Insights
MicroRNA (miRNA) profiles are significantly altered in intraocular medulloepithelioma (ME) tumors compared to normal tissue. These dysregulated miRNAs show similarities to those found in other cancers, impacting pathways like Toll-like receptor and NF-κB signaling.
Area of Science:
- Ophthalmology
- Oncology
- Molecular Biology
Background:
- Intraocular medulloepithelioma (ME) is a rare eye tumor.
- MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression and are implicated in various cancers.
- Understanding miRNA profiles in ME can provide insights into tumor development and potential therapeutic targets.
Purpose of the Study:
- To investigate and compare the microRNA (miRNA) expression profiles between intraocular medulloepithelioma (ME) tumors and normal ocular control tissues.
- To identify specific differentially expressed miRNAs in ME tumors.
Main Methods:
- Total RNA was extracted from formalin-fixed paraffin-embedded (FFPE) ME tumors (n=7) and age-matched ciliary body control tissues (n=8).
- MicroRNA profiles were analyzed using Affymetrix GeneChip miRNA Arrays.
- Quantitative real-time PCR (RT-PCR) was used for validation of significantly dysregulated miRNAs.
- Enrichment analysis of differentially expressed (DE) miRNA gene targets was performed using DIANA-miRPath v2.0 for KEGG pathway analysis.
Main Results:
- A total of 88 miRNAs were significantly upregulated and 43 were downregulated in ME tumors (P<0.05).
- Validation confirmed dysregulation of specific miRNAs including miR-217, miR-216a, miR-216b, miR-146a, miR-509-3p, and miR-211.
- DE miRNAs in ME tumors showed altered expression patterns similar to those in retinoblastoma, glioblastoma, and human cartilage.
- Pathway analysis revealed associations of upregulated miRNAs with prion disease and cancer pathways.
- Downregulated miRNAs were significantly linked to Toll-like receptor (TLR) and Nuclear Factor kappa B (NF-κB) signaling pathways.
Conclusions:
- Intraocular ME tumors exhibit significantly dysregulated miRNA profiles.
- These aberrant miRNA profiles share commonalities with those observed in other cancers, including retinoblastoma and glioblastoma.
- The identified dysregulated pathways suggest potential roles in ME tumorigenesis and provide avenues for further research.
