Interrelation between miRNA and mRNA expression in HT-29 line cells under hypoxia

Nersisyan SA1, Galatenko AV2,3, Maltseva DV1,4, Ushkaryov YuA1, Tonevitsky AG1,4
About authors

1 National Research University Higher School of Economics, Moscow, Russia

2 Lomonosov Moscow State University, Moscow, Russia

3 Moscow Center for Fundamental and Applied Mathematics, Moscow, Russia

4 Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia

Correspondence should be addressed: Diana V. Maltseva
Vavilova, 7, Moscow, 117321; moc.liamg@avestlamd

About paper

Funding: the work was supported financially by the Russian Science Foundation (agreement #17-14-01338).

Compliance with ethical standards: the study was approved by the Ethics Committee of Amur State Medical Academy (Protocol № 10 dated November 20, 2019); the study conformed with the guidelines for the medical research involving human subjects. Voluntary informed consent was obtained from all the participants.

Author contribution: SA Nersisyan and AV Galatenko — sequencing data processing, bioinformatic analysis, functional gene analysis, building the regulatory network of interactions, manuscript preparation; DV Maltseva — cell culturing work, preparation of samples for sequencing, manuscript preparation for publication; YA Ushkaryov — discussion of the results, article text review; AG Tonevitsky — research organization, analysis of the results, article manuscript preparation.

Received: 2020-10-26 Accepted: 2020-11-22 Published online: 2020-12-07

Hypoxia accompanies various pathophysiological processes, including progression of tumors and metastasis. One of the mechanisms of molecular response of cells to hypoxia implies recruitment of specific miRNAs that regulate the expression of their target genes. This study aimed to evaluate the hypoxia-induced change in expression of miRNAs and their target genes in the HT-29 human colorectal adenocarcinoma cell line with the help of integrated miRNA and mRNA sequencing. To simulate hypoxia, the cells were treated with cobalt (II) chloride. We registered a significant change in expression of sixteen human miRNAs. Six of them (hsa-miR-18a-5p, hsa-miR-22-3p, hsa-miR-27a-5p, hsa-miR-182-5p, hsa-miR-215 -5p, hsa-miR-425-5p) had a significant proportion of target genes that had the expression changing in the opposite direction. Based on the bioinformatic analysis of interactions between differentially expressed transcription factors and miRNAs, we built a possible regulatory network with its main hubs being HIF-1α, p65, с-Myc, and Egr1 (encoded by the HIF1A, RELA, MYC and EGR1 genes).

Keywords: hypoxia, miRNA, intestinal epithelium, mRNA, transcriptome, sequencing, HIF-1α, HT-29