Genome-Wide Small RNA Sequencing Identifies MicroRNAs Deregulated in Non-Small Cell Lung Carcinoma Harboring Gain-of-Function Mutant p53.

Arindam Datta,Susanta Roychoudhury,Sangeeta Ghuwalewala,Sanjib Dey,Raghunath Chatterjee,Pijush Das,Sk Kayum Alam,Dishari Ghatak

doi:10.3390/genes10110852

Abstract

Mutations in the TP53 gene are one of the most frequent events in cancers. Certain missense mutant p53 proteins gain oncogenic functions (gain-of-functions) and drive tumorigenesis. Apart from the coding genes, a few non-coding microRNAs (miRNAs) are implicated in mediating mutant p53-driven cancer phenotypes. Here, we identified miRNAs in mutant p53R273H bearing non-small cell lung carcinoma (NSCLC) cells while using small RNA deep sequencing. Differentially regulated miRNAs were validated in the TCGA lung adenocarcinoma patients with p53 mutations and, subsequently, we identified specific miRNA signatures that are associated with lymph node metastasis and poor survival of the patients. Pathway analyses with integrated miRNA-mRNA expressions further revealed potential regulatory molecular networks in mutant p53 cancer cells. A possible contribution of putative mutant p53-regulated miRNAs in epithelial-to-mesenchymal transition (EMT) is also predicted. Most importantly, we identified a novel miRNA from the unmapped sequencing reads through a systematic computational approach. The newly identified miRNA promotes proliferation, colony-forming ability, and migration of NSCLC cells. Overall, the present study provides an altered miRNA expression profile that might be useful in biomarker discovery for non-small cell lung cancers with TP53 mutations and discovers a hitherto unknown miRNA with oncogenic potential.

Highlights

Mutations in the tumor suppressor TP53 gene influence cancer progression and clinical outcomes of human cancers [1,2]
The differentially regulated miRNAs were subjected to pathway analysis while using the Ingenuity Pathway Analysis tool (IPA; https://analysis.ingenuity.com) to gain further insight into the biological changes that they could impart in mutant p53 cells
Identification of miRNAs regulated by mutant p53 on a global scale would provide further insights into the cellular pathways and biological functions that are governed by GOF mutant p53 in the context of tumorigenesis

Summary

Introduction

Mutations in the tumor suppressor TP53 gene influence cancer progression and clinical outcomes of human cancers [1,2]. Most of these mutations are monoallelic missense point mutations that result in the synthesis of full length mutant p53 proteins with altered functions [3]. These mutations generally occur at high frequencies in six “hot spot” amino acid residues [3] of the central DNA-binding domain of p53, which causes a loss of its sequence-specific DNA-binding activity. By cooperating with other transcription factors, such as NF-Y and Sp1, mutant p53 is recruited to target promoters and it facilitates the transcription of the respective genes [9]

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