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Discovery of differentially expressed novel miRNAs in breast normal cells and their putative targets

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Abstract

MicroRNAs (miRNAs) play critical role in normal breast development and their altered expression may lead to breast cancer. Identification of new miRNAs allows us to understand the normal physiological process and associated disease pathophysiology. In the present study we identify the novel miRNAs in withaferin A treated breast normal cells (MCF-10A) using small RNA sequencing. The pathophysiological potential of the identified miRNAs was checked by studying their expression pattern in MDA-MB-231 and MCF-7 breast cancer cells using qRT-PCR technique. The secondary/tertiary structure of the identified miRNAs, target gene enrichment in Gene Ontology terms and KEGG pathway, miRNA-mRNA interaction of the sorted target genes, miRNA-mRNA/miRNA-argonaute protein/miRNA-mRNA-argonaute protein interaction and stability, were studied using bioinformatics tools/software, and molecular dynamics simulations. Hsa-miR-N88585 and hsa-miR-N461089 were identified and validated as novel miRNAs in normal breast cells. Up-expression of identified miRNAs in MDA-MB-231 and MCF-7 cells indicates their oncogenic nature. Identified target genes were enriched in classical signaling pathways (AMPK and Ras) and important GO terms. PLXDC2, BHLHE40, ARMC8, and PECAM1, CDC27, KCNK3 genes were sorted as putative targets for hsa-miR-N88585 and hsa-miR-N461089, respectively. MD simulation revealed stable hsa-miR-N88585/hsa-miR-N461089-AGO protein complex formation which indicates their further processing. In conclusion, the study identifies hsa-miR-N88585 and hsa-miR-N461089 as novel miRNAs in breast normal cells which are significantly inversely expressed in breast cancer cells. Further experiments are required to study the role of identified novel miRNAs in normal breast development and pathophysiology of breast cancer.

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Data availability

The data that support the findings of this study are available in the supplementary material of this article and raw NGS data that were generated in the experiment was deposited in NCBI Gene Expression Omnibus (NCBI-GEO) accessible through GEO accession number GSE180247.

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Acknowledgements

S.K. acknowledges the Department of Science and Technology, India for providing financial support in the form of the DST-SERB Grant [EEQ/2016/000350]. S.K. also acknowledges DST-India for providing a Departmental grant to the Department of Biochemistry, Central University of Punjab, Bathinda, India in the form of the DST-FIST grant. K.S.P. and A.K.S acknowledge DBT, India and CSIR-India for providing financial assistance in the form of Senior Research Fellowship.

Funding

This work was supported by Department of Science and Technology, India for providing financial support in the form of the DST-SERB Grant [EEQ/2016/000350].

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Authors and Affiliations

  1. Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, 151401, India

    Mohd Shuaib, Kumari Sunita Prajapati, Atul Kumar Singh & Shashank Kumar

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  2. Kumari Sunita Prajapati
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SK designed the study, SK supervised all analyses and experiment, MS, KSP and AKS performed the experiments, SK, MS, and KSP performed statistical analysis, SK wrote the first draft of the manuscript. All the authors have read and accepted the final version of the manuscript.

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Correspondence to Shashank Kumar.

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Shuaib, M., Prajapati, K.S., Singh, A.K. et al. Discovery of differentially expressed novel miRNAs in breast normal cells and their putative targets. Mol Cell Biochem 478, 2361–2378 (2023). https://doi.org/10.1007/s11010-023-04665-8

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