Integrated multi-omic analysis of human retinoblastoma identifies novel regulatory networks
Abstract
Purpose
a) Elucidate the differential expression profiles in tumors & invitro models. b) Identify novel signal transductions and key regulators in retinoblastoma.
Methods
Institutional Ethics Committee approval was obtained prior to sample collection. We used enucleated eyes of 9 case samples & 2 pediatric deceased controls. Total RNA was extracted from tumor & control retina samples for mRNA, miRNA microarray and RT-PCR for gene expression validation in tumors. Patient's aqueous, vitreous and tears were analysed by LC/GC-MS to validate metabolic profiles of retinoblastoma. RB invitro models were developed using cell lines MCF-7, Y79 & Weri, for correlative analysis with patient data.
Results
We identified 8 key differentially regulated pathways and genes, from the mRNA expression profile. The miRNA expression profile helps to discover 18 novel miRNAs which regulates key target genes identified by mRNA microarrays. Multi- omics analysis of metabolomics data with gene expression profiles revealed key regulators belonging to common pathways. RB1 silenced MCF-7 showed significant overlap in key cell cycle genes & RB1 complemented retinoblastoma cell line Y79 mimics gain of function of molecular signature.
Conclusions
Overall, the study identifies molecular mechanisms driving retinoblastoma and provides an in-vitro modelling framework for further studies.
