Comparative characteristics of DNA loop domains rearrangement in glioblastoma multiforme T98G and glioblastoma astrocytoma U373 cell lines under different culture conditions

Authors

  • K. Svyrydova Taras Shevchenko National University of Kyiv
  • V. Vasylieva Taras Shevchenko National University of Kyiv
  • S. Kropyvko Institute of Molecular Biology and Genetics
  • K. Afanasieva Taras Shevchenko National University of Kyiv
  • A. Sivolob Taras Shevchenko National University of Kyiv

DOI:

https://doi.org/10.32471/exp-oncology.2312-8852.vol-43-no-4.17080

Keywords:

cell functional state, comet assay, DNA loops, glioblastoma, T98G cell line, U373 cell line

Abstract

Summary. Background: The loop domain organization of chromatin, which plays an important role in transcription regulation, may depend on the cell functional state. The aim of this work was to investigate DNA loop reorganization upon functional transitions in two cell lines ‒ glioblastoma multiforme T98G and glioblastoma astrocytoma U373. Materials and Methods: Single cell gel electrophoresis (the comet assay) was used to analyze the kinetics of the DNA loop migration from the nucleoids obtained from the lysed cells. Results: The DNA fraction in the surface loops and the size of these loops were found to be similar in two glioblastoma cell lines. When synthetic processes were inhibited, the migration of a small portion of inner loops was observed in T98G but not U373 cells. In T98G cells, stimulation of cell proliferation and transcription was accompanied by an increase in DNA fraction in the inner loops and an essential increase in the size of these loops. The effect of stimulation was practically absent in U373 cells. However, the linear density of the loops resolved by the comet assay was found to decrease upon stimulation of proliferation in both cell lines. Conclusion: A decrease in the loop density appears to be associated with an intensification of the synthetic processes in cells upon their stimulation.

References

Bradner JE, Hnisz D, Young RA. Transcriptional addiction in cancer. Cell 2017; 168: 629–43. https://doi.org/10.1016/j.cell.2016.12.013

Ma B, Leijten JCH, Wu L, et al. Gene expression profiling of dedifferentiated human articular chondrocytes in monolayer culture. Osteoarthritis Cartilage 2013; 21: 599–603. https://doi.org/10.1016/j.joca.2013.01.014

Krietenstein N, Abraham S, Venev SV, et al. Ultrastructural details of mammalian chromosome architecture. Mol Cell 2020; 78: 554–65. https://doi.org/10.1016/j.molcel.2020.03.003

Pombo A, Dillon N. Three-dimensional genome architecture: players and mechanisms. Nat Rev Mol Cell Biol 2015; 16: 245–57. https://doi.org/10.1038/nrm3965

Kadauke S, Blobel G. Chromatin loops in gene regulation. Biochim Biophys Acta 2009; 1789: 17–25. https://doi.org/10.1016/j.bbagrm.2008.07.002

Ong CT, Corces VG. CTCF: an architectural protein bridging genome topology and function. Nat Rev Genet 2014; 15: 234–46. https://doi.org/10.1038/nrg3663

Van Bortle K, Corces VG. Nuclear organization and genome function. Annu Rev Cell Dev Biol 2012; 28: 163–87. https://doi.org/10.1146/annurev-cellbio-101011-155824

Kieffer-Kwon KR, Nimura K, Rao SSP, et al. Myc regulates chromatin decompaction and nuclear architecture during B cell activation. Mol Cell 2017; 67: 566–78. https://doi.org/10.1016/j.molcel.2017.07.013

Afanasieva KS, Chopei MI, Lozovik AV, et al. Redistribution of DNA loop domains in human lymphocytes under blast transformation with interleukin 2. Ukr Biochem J 2016; 88: 45–51. doi: https://doi.org/10.15407/ubj88.06.045

Afanasieva K, Olefirenko V, Martyniak A, et al. DNA loop domain rearrangements in blast transformed human lymphocytes and lymphoid leukaemic Jurkat T cells. Ukr Biochem J 2020; 5: 62–89. doi: https://doi.org/10.15407/ubj92.05.062

Afanasieva K, Zazhytska M, Sivolob A. Kinetics of comet formation in single-cell gel electrophoresis: loops and fragments. Electrophoresis 2010; 31: 512–9. https://doi.org/10.1002/elps.200900421

Afanasieva K, Chopei M, Zazhytska M, et al. DNA loop domain organization as revealed by single-cell gel electrophoresis. Biochim Biophys Acta 2013; 1833: 3237–44. https://doi.org/10.1016/j.bbamcr.2013.09.021

Afanasieva K, Chopei M, Lozovik A, et al. DNA loop domain organization in nucleoids from cells of different types. Biochem Biophys Res Commun 2017; 483: 142–6. https://doi.org/10.1016/j.bbrc.2016.12.177

Afanasieva KS, Sivolob AV. Kіnetic approach in comet assay: an opportunity to investigate DNA loops. In: Harmon KH, eds. A Closer Look at the Comet Assay. New York City, New York, United States of America: Nova Science Publishers, 2019: 65–84.

Stein GH. T98G: an anchorage-independent human tumor cell line that exhibits stationary phase G1 arrest in vitro. J Cell Physiol 1979; 99: 43–54. https://doi.org/10.1002/jcp.1040990107

Kim S, Seo Y, Chowdhury T, et al. Inhibition of MUC1 exerts cell-cycle arrest and telomerase suppression in glioblastoma cells. Sci Rep 2020; 10: 18238. https://doi.org/10.1038/s41598-020-75457-z

Pucko E, Ostrowski R, Matyja E. Novel small molecule protein kinase CK2 inhibitors exert potent antitumor effects on T98G and SEGA cells in vitro. Folia Neuropathol 2019; 57: 239–48. https://doi.org/10.5114/fn.2019.88452

Kiseleva LN, Kartashev AV, Vartanyan NL, et al. A172 and T98G cell lines characteristics. Cell Tiss Biol 2016; 10: 341–8. https://doi.org/10.1134/S1990519X16050072

Westermark B, Pontén J, Hugosson R. Determinants for the establishment of permanent tissue culture lines from human gliomas. Acta Pathol Microbiol Scand 1973; 81: 791–805. https://doi.org/10.1111/j.1699-0463.1973.tb03573.x

Bigner SH, Bullard DE, Pegram CN, et al. Relationship of in vitro morphologic and growth characteristics of established human glioma-derived cell lines to their tumorigenicity in athymic nude mice. J Neuropathol Exp Neurol 1981; 40: 390–409. https://doi.org/10.1097/00005072-198107000-00004

Nistér M, Westermark B. Human Glioma Cell Lines. In: Hay RJ, Park JG, Gazdar A, eds. Atlas of Human Tumor Cell Lines. Cambridge, Massachusetts, United States of America: Academic Press, 1994: 17–42. https://doi.org/10.1016/B978-0-12-333530-2.50005-8

Afanasieva KS, Semenova AY, Lukash LL, et al. DNA loop organization in glioblastoma T98G cells at their different functional states. Biopolym Сell 2018; 34: 426–34. https://doi.org/10.7124/bc.00098D

Dell’orco RT, Crissman HA, Steinkamp JA, et al. Population analysis of arrested human diploid fibroblasts by flow microfluorometry. Exp Cell Res 1975; 92: 271–4. https://doi.org/10.1016/0014-4827(75)90380-8

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Published

26.05.2023

How to Cite

Svyrydova, K., Vasylieva, V., Kropyvko, S., Afanasieva, K., & Sivolob, A. (2023). Comparative characteristics of DNA loop domains rearrangement in glioblastoma multiforme T98G and glioblastoma astrocytoma U373 cell lines under different culture conditions. Experimental Oncology, 43(4), 306–311. https://doi.org/10.32471/exp-oncology.2312-8852.vol-43-no-4.17080

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Vol. 43 No. 4 (2021): Experimental Oncology

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