Identification and Insilico Analysis of Retinoblastoma Serum microRNA Profile and Gene Targets towards Prediction of Novel Serum Biomarkers

Abstract

Retinoblastoma (RB) is a malignant tumor of the retina seen in children, and potential non invasive biomarkers are in need for rapid diagnosis and for prognosticating the therapy. This study was undertaken to identify the differentially expressed miRNAs in the serum of children with RB in comparison with the normal age matched serum, to analyze its concurrence with the existing RB tumor miRNA profile, to identify its novel gene targets specific to RB, and to study the expression of a few of the identified oncogenic miRNAs in the advanced stage primary RB patient’s serum sample. MiRNA profiling was performed on 14 pooled serum from children with advanced RB and 14 normal age matched serum samples, wherein 21 miRNAs were found to be upregulated (fold change ≤ −2.0, P ≤ 0.05) and 24 to be downregulated (fold change ≥ +2.0, P ≤ 0.05). Furthermore, intersection of 59 significantly deregulated miRNAs identified from RB tumor profiles with that of miRNAs detected in serum profile revealed that 33 miRNAs had followed a similar deregulation pattern in RB serum. Later we validated a few of the miRNAs (miRNA 17-92) identified by microarray in the RB patient serum samples (n = 20) by using qRT-PCR. Expression of the oncogenic miRNAs, miR-17, miR-18a, and miR-20a by qRT-PCR was significant in the serum samples exploring the potential of serum miRNAs identification as noninvasive diagnosis. Moreover, from miRNA gene target prediction, key regulatory genes of cell proliferation, apoptosis, and positive and negative regulatory networks involved in RB progression were identified in the gene expression profile of RB tumors. Therefore, these identified miRNAs and their corresponding target genes could give insights on potential biomarkers and key events involved in the RB pathway.

Clinical Significance of Upregulation of mir-196a-5p in Gastric Cancer and Enriched KEGG Pathway Analysis of Target Genes

“…In recent years, this kind of combination analysis of any identified miRNA, its corresponding target genes, enriched KEGG pathways, and even miRNAmRNA network were performed in cancer studies (Satoh, 2012;Liu et al, 2014), particularly in cancer biomarker discoveries (Romero-Cordoba et al, 2012;Beta et al, 2013). In this study, based on miRWalk database combined with DAVID 6.7 tool and mirfocus 3.0, bioinformatics prediction and Enriched KEGG pathways analysis of miR-196a-5p indicated that both predicted target genes and validated target genes of miR-196a were clustered in cancer associated KEGG pathways.…”

microRNA-497 overexpression decreases proliferation, migration and invasion of human retinoblastoma cells via targeting vascular endothelial growth factor A

“…In 2015, it was estimated that there were 2,580 new cases in the United States (3). Various factors are involved in the carcinogenesis and development of retinoblastoma, including genetic and epigenetic alterations to oncogenes and tumor suppressor genes, and a large number of these have previously been demonstrated to regulate cell growth, the cell cycle and apoptosis (4,5). In developed countries, >95% of patients with retinoblastoma have a good prognosis.…”

PMMA Platform Based Micro Fluidic Mixer for the Detection of MicroRNA- 18a from Retinoblastoma Serum

“…While each tumor type is characterized by its own unique miRNA profile, it is interesting to note that several miRNAs appear to be up-or down-regulated in almost all tumor samples relative to normal adjacent tissue. Beta et al [15] studied the miRNA profile of RB sample using in silico methods and found that 21 miRNAs are upregulated and 24 are down regulated in RB.…”