MicroRNA profiling in intraocular medulloepitheliomas

Deepak P Edward; Hind Alkatan; Qundeel Rafiq; Charles Eberhart; Saleh Al Mesfer; Nicola Ghazi; Leen Al Safieh; Altaf A Kondkar; Khaled K Abu Amero

doi:10.1371/journal.pone.0121706

MicroRNA profiling in intraocular medulloepitheliomas

PLoS One. 2015 Mar 25;10(3):e0121706. doi: 10.1371/journal.pone.0121706. eCollection 2015.

Authors

Deepak P Edward¹, Hind Alkatan², Qundeel Rafiq³, Charles Eberhart³, Saleh Al Mesfer², Nicola Ghazi², Leen Al Safieh², Altaf A Kondkar⁴, Khaled K Abu Amero⁵

Affiliations

¹ King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia; Wilmer Eye Institute, John Hopkins University School Of Medicine, Baltimore, MD, United States of America.
² King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia.
³ Wilmer Eye Institute, John Hopkins University School Of Medicine, Baltimore, MD, United States of America.
⁴ Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.
⁵ Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia; Department of Ophthalmology, College of Medicine, University of Florida, Jacksonville, FL, United States of America.

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adolescent
Case-Control Studies
Child
Child, Preschool
Down-Regulation / genetics
Female
Gene Expression Profiling / methods
Humans
Infant
Male
MicroRNAs / genetics*
NF-kappa B / genetics
Neuroectodermal Tumors, Primitive / genetics*
Signal Transduction / genetics
Toll-Like Receptors / genetics
Transcriptome / genetics*
Up-Regulation / genetics

Substances

MicroRNAs
NF-kappa B
Toll-Like Receptors

Grants and funding

This study was funded by the KKESH-JHU collaborative grant KKESHJHU/02-04. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.