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Differential transcriptome analysis in HPV-positive and HPV-negative cervical cancer cells through CRISPR knockout of miR-214

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Abstract

In this study we have investigated the effects of a tumour suppressor microRNA, miR-214, on gene expression in HPV-positive (CaSki) and HPV-negative cervical cancer cells (C33A) by RNA sequencing using next generation sequencing. The HPV-positive and HPV-negative cervical cancer cells were either miR-214-knocked-out or miR-214-overexpressed. Gene expression analysis showed that a total of 904 genes were upregulated and 365 genes were downregulated between HPV-positive and HPV-negative cervical cancer cells with a fold change of ±2. Furthermore, 11 differentially expressed and relevant genes (TNFAIP3, RAB25, MET, CYP1B1, NDRG1, CD24, LOXL2, CD44, PMS2, LATS1 and MDM1) which showed a fold change of ±5 were selected to confirm by real-time PCR. This study represents the first report of miR-214 on global gene expression in the context of HPV.

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Abbreviations

3ʹ-UTR:

3ʹ-untranslated region

ATCC:

American Type Culture Collection

CC:

cervical cancer

CIN:

cervical intraepithelial neoplasia

CRISPR:

clustered regularly interspaced short palindromic repeats

DAVID:

the database for annotation, visualization and integrated discovery

DEG:

differentially expressed genes

DMEM:

Dulbecco’s Modified Eagle Medium

FBS:

fetal bovine serum

GO:

gene ontology

KEGG:

Kyoto Encyclopedia of Genes and Genomes

miR:

microRNA

NGS:

Next Generation sequencing

NIAID:

National Institute of Allergy and Infectious Diseases

qRT-PCR:

quantitative real-time PCR

RIN:

RNA integrity number

RNA-seq:

RNA-sequencing

sgRNA:

single guide RNA

SRA:

sequence read archive

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Acknowledgements

The funding from SERB, India, is duly acknowledged.

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Authors and Affiliations

  1. Cancer Biology Lab, School of Biotechnology, KIIT University, Bhubaneswar, India

    Prakriti Sen, Pooja Ganguly & Niladri Ganguly

  2. Bionivid Technology Pvt. Ltd., Kasturi Nagar, Bengaluru, India

    Kirti K Kulkarni & Roli Budhwar

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  1. Prakriti Sen
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  2. Pooja Ganguly
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  3. Kirti K Kulkarni
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  4. Roli Budhwar
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  5. Niladri Ganguly
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Corresponding author

Correspondence to Niladri Ganguly.

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Communicated by Saumitra Das.

Editorial Responsibility: Saumitra Das

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Sen, P., Ganguly, P., Kulkarni, K.K. et al. Differential transcriptome analysis in HPV-positive and HPV-negative cervical cancer cells through CRISPR knockout of miR-214. J Biosci 45, 104 (2020). https://doi.org/10.1007/s12038-020-00075-w

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