Prediction of novel polymorphisms in micrornas targeting the rit2 interactions network: a bioinformatics approach

Zahra Bahmanpour,1 Yousef daneshmandpour,2 Fatemeh radnia,3 Bahare khademi,4 Mahsa tahmasebi,5 Babak emamalizadeh,6,*

1. Students Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
2. Students Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
3. Students Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
4. Students Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
5. Students Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
6. Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran

Abstract

Introduction

Rit2 protein is a neuron-specific small guanosine triphosphatase and a member of the ras superfamily that has been proved to be expressed in a subset of neurons including retinal ganglion cells (rgcs) and selected neurons in the brain. rit2 has also been indicated to have important roles in neuronal differentiation and function. multiple variations in different neurologic and psychiatric disorders have been reported in rit2 gene and its correlated network. mirnas and single nucleotide polymorphisms (snp) located in mirna coding genes or their target sites have been developed as a class of variants conferring susceptibility to various disease. to date, no study has yet analyzed the possible effect of mirnas and mir-snps on rit2 and its network. so, in the current study we have conducted an in-silico study in order to predict the possible role of mirnas and mir-snps on rit2 network.

Methods

At first, in order to explore the network of interactions of rit2, pathway commons database was applied and its related genes were selected and were reviewed in articles to ensure their roles in neurological disorders. then, mirnas that target the genes involved in this network are identified thorough mirtarbase, tarbase, target scan and other similar databases. subsequently, mirdsnp, dbsnp and mirsnp databases were employed for identifying mirsnps affecting candidate genes.

Results

The resulting mirna: mrna: snps were further evaluated for the functional evidences supporting their involvement in rit2 network interaction. the analysis showed that some mirsnps in selected genes’ seed regions including hsa-mir-3163: rit2: rs140706543, hsa-mir-200c-3p: ntrk2: rs77542010, hsa-mir-124-3p: bdnf: rs11030100, hsa-mir-4680-3p: atp12a: rs2722, hsa-mir-548as-3p: rfx1: rs115028104, hsa-mir-615-3p: tcf3: rs113708250, hsa-mir-485-3p: ntrk3:rs28521337, hsa-mir-548as-3p: tfap4 : rs417083 may potentially contribute to the pathogenesis of neurological disorders.

Conclusion

Rit2 and its network play important role in neuron cells and has been contributed to multiple neurologic disorders. in current study we have predicted possible role of mirnas and mir-snps in rit2 and its correlated network. these predictions may be good experimental targets in order to find new biomarkers for neurologic diseases. but, further experimental studies are required to validate the achieved results.

Keywords

Mirnas, mir-snps, rit2, neurodegenerative disorder, psychiatric disorder, bioinformatics