“Биполярное” действие ингибитора васкулогенной мимикрии на экспрессию генов в клетках меланомы

封面

如何引用文章

全文:

开放存取 开放存取
受限制的访问 ##reader.subscriptionAccessGranted##
受限制的访问 订阅存取

详细

Multiple exogenous or endogenous factors alter gene expression patterns by different mechanisms that yet are poorly understood. We used RNA-Seq analysis in order to study changes in gene expression in melanoma cells capable to vasculogenic mimicry upon action of inhibitor of vasculogenic mimicry. Here, we describe that the drug induces a strong upregulation of 50 genes controlling cell cycle and microtubule cytoskeleton coupled with a strong downregulation of 50 genes controlling different cellular metabolic processes. We found that both groups of genes are simultaneously regulated by multiple sets of transcription factors. We conclude, that one way for coordinated regulation of big groups of genes is the regulation simultaneously by multiple transcription factors.

全文:

受限制的访问

作者简介

N. Tchurikov

Engelhardt Institute of Molecular Biology Russian Academy of Science

编辑信件的主要联系方式.
Email: tchurikov@eimb.ru
俄罗斯联邦, Moscow, 119991

A. Vartanian

Department of Experimental Diagnosis and Therapy of Tumors, N. N. Blokhin National Medical Research Center of Oncology, Ministry of Health of Russia

Email: tchurikov@eimb.ru
俄罗斯联邦, Moscow, 115478

E. Klushevskaya

Engelhardt Institute of Molecular Biology Russian Academy of Sciences

Email: tchurikov@eimb.ru
俄罗斯联邦, Moscow, 119991

I. Alembekov

Engelhardt Institute of Molecular Biology Russian Academy of Sciences

Email: tchurikov@eimb.ru
俄罗斯联邦, Moscow, 119991

A. Kretova

Engelhardt Institute of Molecular Biology Russian Academy of Sciences

Email: tchurikov@eimb.ru
俄罗斯联邦, Moscow, 119991

V. Сhechetkin

Engelhardt Institute of Molecular Biology Russian Academy of Sciences

Email: tchurikov@eimb.ru
俄罗斯联邦, Moscow, 119991

G. Kravatskaya

Engelhardt Institute of Molecular Biology Russian Academy of Sciences

Email: tchurikov@eimb.ru
俄罗斯联邦, Moscow, 119991

V. Kosorukov

Department of Experimental Diagnosis and Therapy of Tumors, N. N. Blokhin National Medical Research Center of Oncology, Ministry of Health of Russia

Email: tchurikov@eimb.ru
俄罗斯联邦, Moscow, 115478

Yu. Kravatsky

Engelhardt Institute of Molecular Biology Russian Academy of Sciences

Email: tchurikov@eimb.ru
俄罗斯联邦, Moscow, 119991

参考

  1. Kosak S.T., Scalzo D., Alworth S.V., Li F., Palmer S., Enver T., Lee J.S., Groudine M. (2007) Coordinate gene regulation during hematopoiesis is related to genomic organization. PLoS Biol. 5(11), e309. https://doi.org/10.1371/journal.pbio.0050309
  2. Tchurikov N.A., Fedoseeva D.M., Sosin D.V., Snezhkina A.V., Melnikova N.V., Kudryavtseva A.V., Kravatsky Y.V., Kretova O.V. (2015) Hot spots of DNA double-strand breaks and genomic contacts of human rDNA units are involved in epigenetic regulation. J. Mol. Cell. Biol. 7, 366‒382. doi: 10.1093/jmcb/mju038
  3. Xu P., Wu Q., Yu J., Rao Y., Kou Z., Fang G., Shi X., Liu W., Han H. (2020) A systematic way to infer the regulation relations of miRNAs on target genes and critical miRNAs in cancers. Front. Genet. 11, 278. doi: 10.3389/fgene.2020.00278
  4. Tchurikov N.A., Kretova O.V. (2007) Suffix-specific RNAi leads to silencing of F element in Drosophila melanogaster. PLoS One. 2(5), e476. doi: 10.1371/journal.pone.0000476
  5. Bartel D.P. (2018) Metazoan microRNAs. Cell. 173, 20–51. doi: 10.1016/j.cell.2018.03.006
  6. Vartanian A., Baryshnikova M., Burova O., Afanasyeva D., Misyurin V., Belyаvsky A., Shprakh Z. (2017) Inhibitor of vasculogenic mimicry restores sensitivity of resistant melanoma cells to DNA-damaging agents. Melanoma Res. 27, 8‒16. doi: 10.1097/CMR.0000000000000308
  7. Kalitin N.N., Ektova L.V., Kostritsa N.S., Sivirinova A.S., Kostarev A.V., Smirnova G.B., Borisova Y.A., Golubeva I.S., Ermolaeva E.V., Vergun M.A., Babaeva M.A., Lushnikova A.A., Karamysheva A.F. (2022) A novel glycosylated indolocarbazole derivative LCS1269 effectively inhibits growth of human cancer cells in vitro and in vivo through driving of both apoptosis and senescence by inducing of DNA damage and modulating of AKT/mTOR/S6K and ERK pathways. Chem. Biol. Interact. 364, 10056. doi: 10.1016/j.cbi.2022.110056
  8. Maniotis A.J., Folberg R., Hess A., Seftor E.A., Gardner L.M., Pe’er J., Trent J.M., Meltzer P.S., Hendrix M.J. (1999) Vascular channel formation by human melanoma cells in vivo and in vitro: vasculogenic mimicry. Am. J. Pathol. 155(3), 739–752. doi: 10.1016/S0002-9440(10)65173-5
  9. Вартанян А., Хоченкова Ю., Кособокова Е., Барышникова М., Косоруков В. (2021) СД437 снижает метастатический потенциал клеток меланомы. Вестн. Моск. Ун-та. Сер. 2. Химия. 62(4), 333–340.
  10. Ramirez F., Ryan D.P., Gruning B., Bhardwaj V., Kilpert F., Richter A.S., Heyne S., Dundar F., Manke T. (2016) deepTools2: a next generation web server for deep-sequencing data analysis. Nucl. Acids Res. 44, W160–165.
  11. Cui H., Zhao J. (2020) LncRNA TMPO-AS1 serves as a ceRNA to promote osteosarcoma tumorigenesis by regulating miR-199a-5p/WNT7B axis. J. Cell Biochem. 121, 2284–2293. doi: 10.1002/jcb.2945110
  12. Gkika D., Lemonnier L., Shapovalov G., Gordienko D., Poux C., Bernardini M., Bokhobza A., Bidaux G., Degerny C., Verreman K., Guarmit B., Benahmed M., de Launoit Y., Bindels R.J., Fiorio Pla A., Prevarskaya N. (2015) TRP channel-associated factors are a novel protein family that regulates TRPM8 trafficking and activity. J. Cell Biol. 208, 89–107. 10.1083/jcb.201402076' target='_blank'>https://doi: 10.1083/jcb.201402076
  13. Hu F., Fong K.O., Cheung M.P.L., Liu J.A., Liang R., Li T.W., Sharma R., Ip P.P., Yang X., Cheung M. (2022) DEPDC1B promotes melanoma angiogenesis and metastasis through sequestration of ubiquitin ligase CDC16 to stabilize secreted SCUBE3. Adv. Sci. 9, 2105226. https://doi.org/10.1002/advs.202105226
  14. Xu Y., Sun W., Zheng B., Liu X., Luo Z., Kong Y., Xu M., Chen Y. (2019) DEPDC1B knockdown inhibits the development of malignant melanoma through suppressing cell proliferation and inducing cell apoptosis. Exp. Cell. Res. 379(1), 48–54. doi: 10.1016/j.yexcr.2019.03.021
  15. Musa J., Aynaud M.M., Mirabeau O., Delattre O., Grünewald T.G. (2017) MYBL2 (B-Myb): a central regulator of cell proliferation, cell survival and differentiation involved in tumorigenesis. Cell Death Dis. 8, e2895 (2017). https://doi.org/10.1038/cddis.2017.244
  16. Thurlings I., Martínez-López L., Westendorp B., Hien B.T., Martínez-López L.M., Zijp M., Thurlings I., Thomas R.E., Schulte-Merker S., Bakker W.J., de Bruin A. (2017) Synergistic functions of E2F7 and E2F8 are critical to suppress stress-induced skin cancer. Oncogene. 36, 829–839. https://doi.org/10.1038/onc.2016.251
  17. Vartanian A., Stepanova E., Grigorieva I., Solomko E., Belkin V., Baryshnikov A., Lichinitser M. (2011) Melanoma vasculogenic mimicry capillary-like structure formation depends on integrin and calcium signaling. Microcirculation. 18, 390–399. doi: 10.1111/j.1549-8719.2011.00102.x
  18. Bera K., Kiepas A., Godet I., Li Y., Mehta P., Ifemembi B., Paul C.D., Sen A., Serra S.A., Stoletov K., Tao J., Shatkin G., Lee S.J., Zhang Y., Boen A., Mistriotis P., Gilkes D.M., Lewis J.D., Fan C.M., Feinberg A.P., Valverde M.A., Sun S.X., Konstantopoulos K. (2022) Extracellular fluid viscosity enhances cell migration and cancer dissemination. Nature. 611, 365–373. https://doi.org/10.1038/s41586-022-05394-6
  19. Lachmann A., Torre D., Keenan A.B., Jagodnik K.M., Lee H.J., Wang L., Silverstein M.C., Ma’ayan A. (2018) Massive mining of publicly available RNA-seq data from human and mouse. Nat. Commun. 9, 1366.
  20. Tchurikov N.A., Klushevskaya E.S., Alembekov I.R., Kretova A.N., Chechetkin V.R., Kravatskaya G.I., Kravatsky Y.V. (2023) Induction of the erythroid differentiation of K562 Cells is coupled with changes in the inter-chromosomal contacts of rDNA clusters. Int. J. Mol. Sci. 24(12), 9842. https://doi.org/10.3390/ijms24129842

补充文件

附件文件
动作
1. JATS XML
下载
2. Fig. 1. Heat map of gene expression changes in melanoma cells under the influence of a vasculogenic mimicry inhibitor. Fifty genes were selected for each gene whose expression changed maximally (increased or decreased) under the influence of the inhibitor. A color scale of expression changes in log2FC is shown. The 50 genes whose expression increased correspond to the logFC > 1.71 criterion (i.e., their expression increased by more than 3.27 times). The 50 genes whose expression decreased correspond to the log2FC < 1.89 criterion (i.e., their expression decreased by more than 3.7 times).

下载 (189KB)
索引源数据
3. Fig. 2. Genes whose expression changed under the influence of the inhibitor (Input Genes) are regulated simultaneously by many FTs (Enriched Terms). a – Genes whose expression increased. b – Genes whose expression decreased. The results were obtained using the Enrichr database (https://maayanlab.cloud/Enrichr/enrich) to search for FTs that simultaneously regulate genes (Enrichr Submissions TF-Gene Coocurrence).

下载 (270KB)
索引源数据
4. Fig. 3. Schematic showing how adding an inhibitor disrupts the gene expression balance and how this affects the phenotype of melanoma cells. a – Gene expression balance before adding the inhibitor. Spindle-shaped cells on Matrigel form vessel-like structures. b – Disruption of the gene expression balance causes changes in cell behavior (formation of vessel-like structures is disrupted) and their shape (cells are more rounded).

下载 (196KB)
索引源数据

版权所有 © Russian Academy of Sciences, 2024