2020 / 06

Next Paper
DOI: 10.24075/brsmu.2020.074
Copyright: © 2020 by the authors. Licensee: Pirogov University.
This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (CC BY).

ORIGINAL RESEARCH

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
|
  1. Semenza GL. Hypoxia-inducible factor 1 and cardiovascular disease. Annu Rev Physiol. 2014; 76: 39–56.
  2. Muz B, de la Puente P, Azab F, Azab AK. The role of hypoxia in cancer progression, angiogenesis, metastasis, and resistance to therapy. Hypoxia. 2015; 83.
  3. Muñoz-Sánchez J, Chánez-Cárdenas ME. The use of cobalt chloride as a chemical hypoxia model. J Appl Toxicol. 2019; 39 (4): 556–70.
  4. Cai Y, Yu X, Hu S, Yu J. A Brief Review on the Mechanisms of miRNA Regulation. Genomics Proteomics Bioinformatics. Elsevier; 2009; 7 (4): 147–54.
  5. Hendrickson DG, Hogan DJ, McCullough HL, Myers JW, Herschlag D, Ferrell JE, et al. Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. PLoS Biol. 2009; 7 (11).
  6. Turchinovich A, Tonevitsky AG, Cho WC, Burwinkel B. Check and mate to exosomal extracellular miRNA: new lesson from a new approach. Front Mol Biosci. Frontiers; 2015; 2: 11.
  7. Visone R, Croce CM. MiRNAs and cancer. Am J Pathol. 2009; 174 (4): 1131–8.
  8. Shkurnikov M, Nikulin S, Nersisyan S, Poloznikov A, Zaidi S, Baranova A, et al. LAMA4-Regulating miR-4274 and Its Host Gene SORCS2 Play a Role in IGFBP6-Dependent Effects on Phenotype of Basal-Like Breast Cancer. Front Mol Biosci. 2019; 6.
  9. Lacedonia D, Scioscia G, Palladino GP, Gallo C, Carpagnano GE, Sabato R, et al. MicroRNA expression profile during different conditions of hypoxia. Oncotarget. 2018; 9 (80): 35114–22.
  10. Shen G, Li X, Jia YF, Piazza GA, Xi Y. Hypoxia-regulated microRNAs in human cancer. Acta Pharmacol Sin. 2013; 34 (3): 336–41.
  11. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal. 2011; 17 (1): 10.
  12. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: Ultrafast universal RNA-seq aligner. Bioinformatics. 2013; 29 (1): 15–21.
  13. Friedländer MR, Mackowiak SD, Li N, Chen W, Rajewsky N. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res. Oxford Academic. 2012; 40 (1): 37–52.
  14. Robinson MD, McCarthy DJ, Smyth GK. edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2009; 26 (1): 139–40.
  15. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. BioMed Central. 2014; 15 (12): 550.
  16. Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. Nature Publishing Group. 2009; 4 (1): 44–57.
  17. Agarwal V, Bell GW, Nam JW, Bartel DP. Predicting effective microRNA target sites in mammalian mRNAs. Elife. 2015; 4 (AUGUST2015).
  18. Muzny DM, Bainbridge MN, Chang K, Dinh HH, Drummond JA, Fowler G, et al. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012; 487 (7407): 330–7.
  19. Tong Z, Cui Q, Wang J, Zhou Y. TransmiR v2.0: An updated transcription factor-microRNA regulation database. Nucleic Acids Res. 2019; 47 (D1): D253--D258.
  20. Culver C, Sundqvist A, Mudie S, Melvin A, Xirodimas D, Rocha S. Mechanism of hypoxia-induced NF-κB. Mol Cell Biol. 2010; 30 (20): 4901–21.
  21. Mungai PT, Waypa GB, Jairaman A, Prakriya M, Dokic D, Ball MK, et al. Hypoxia Triggers AMPK Activation through Reactive Oxygen Species-Mediated Activation of Calcium Release-Activated Calcium Channels. Mol Cell Biol. 2011; 31 (17): 3531–45.
  22. Domogatskaya A, Rodin S, Tryggvason K. Functional Diversity of Laminins. Annu Rev Cell Dev Biol. 2012; 28 (1): 523–53.
  23. Bavelloni A, Ramazzotti G, Poli A, Piazzi M, Focaccia E, Blalock W, et al. Mirna-210: A current overview. Anticancer Res. 2017; 37 (12): 6511–21.
  24. Rankin EB, Giaccia AJ. Hypoxic control of metastasis. Sci (80- ). 2016; 352 (6282): 175–80.
  25. Maltseva D V., Rodin SA. Laminins in metastatic cancer. Mol Biol. Springer; 2018; 52 (3): 350–71.
  26. Kashima H, Wu RC, Wang Y, Sinno AK, Miyamoto T, Shiozawa T, et al. Laminin C1 expression by uterine carcinoma cells is associated with tumor progression. Gynecol Oncol. Elsevier Inc.; 2015; 139 (2): 338–44.
  27. Zhang J, Qiu W, Ma J, Wang Y, Hu Z, Long K, et al. miR-27a- 5p Attenuates Hypoxia-induced Rat Cardiomyocyte Injury by Inhibiting Atg7. Int J Mol Sci. 2019; 20 (10).
  28. Zhang Y, Fang J, Ma H. Inhibition of miR-182-5p protects cardiomyocytes from hypoxia-induced apoptosis by targeting CIAPIN1. Biochem Cell Biol. 2018; 96 (5): 646–54.
  29. Nersisyan S, Engibaryan N, Gorbonos A, Kirdey K, Makhonin A, Tonevitsky A. Potential role of cellular miRNAs in coronavirus-host interplay. PeerJ. 2020; 8: e9994.
  30. Van Kouwenhove M, Kedde M, Agami R. MicroRNA regulation by RNA-binding proteins and its implications for cancer. Nat Rev Cancer. 2011; 11 (9): 644–56.