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Year 2023, , 53 - 61, 26.03.2023

Serap Ozer Yaman , Sema Mısır

https://doi.org/10.17776/csj.1230387

Abstract

Keywords

Biomarker Breast cancer ceRNA miRNA

References

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  • [2] Bray F., Ferlay J., Soerjomataram I., Siegel R.L., Torre L.A., Jemal A., Global cancer statistics 2018:GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries, CA Cancer J Clin.,68(6) (2018) 394-424.
  • [3] Wang L., Early diagnosis of breast cancer, Sensors., 17(7) (2017) 1-20.
  • [4] Loh H. Y., Norman B. P., Lai K. S., Rahman N. M. A. N. A., Alitheen N. B. M., Osman M. A., The regulatory role of microRNAs in breast cancer, Int. J. Mol. Sci., 20(19) (2019) 1-27.
  • [5] Szczepanek J., Skorupa M., Tretyn A., MicroRNA as a potential therapeutic molecule in cancer, Cells, 11(6) (2022) 1-24.
  • [6] Jang J. Y., Kim Y. S., Kang K. N., Kim K. H., Park Y. J., Kim, C. W., Multiple microRNAs as biomarkers for early breast cancer diagnosis, Mol Clin Oncol., 14(2) (2021) 1-9.
  • [7] Qi X., Zhang D.H., Wu N., Xiao J.H., Wang X., Ma W., CeRNA in cancer: possible functions and clinical implications, J Med Genet., 52(10) (2015) 710-8.
  • [8] Fassan M., Dall'Olmo L., Galasso M., Braconi C., Pizzi M., Realdon S., Volinia S., Valeri N., Gasparini P., Baffa R., Souza R.F., Vicentini C., D'Angelo E., Bornschein J., Nuovo G.J., Zaninotto G., Croce C. M., Rugge M., Transcribed ultraconserved noncoding RNAs (TUCR) are involved in Barrett's esophagus carcinogenesis, Oncotarget, 5(16) (2014) 7162-71.
  • [9] Dweep H., Gretz N., miRWalk2. 0: a comprehensive atlas of microRNA-target interactions, Nat Methods., 12 (8) (2015) 697-697.
  • [10] Coronnello C., Benos P.V., ComiR: combinatorial microRNA target prediction tool, Nucleic Acids Res., 41(W1) (2013) W159-W164.
  • [11] Bejerano G., Pheasant M., Makunin I., Stephen S., Kent W.J., Mattick J.S., Haussler D., Ultraconserved elements in the human genome. Science., 304(5675) (2004) 1321-5.
  • [12] Tang Z., Li C., Kang B., GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses, Nucleic Acids Res., 45(W1) (2017) W98-W102
  • [13] Ghoncheh M., Pournamdar Z., Salehiniya H., Incidence and mortality and epidemiology of breast cancer in the world. Asian Pac. J. Cancer Prev, 17(sup3) (2016) 43-46.
  • [14] Bettaieb A., Paul C., Plenchette S., Shan J., Chouchane L., Ghiringhelli F., Precision Medicine in Breast Cancer: Reality or Utopia? J Transl Med, 15 (1) (2017) 1-13.
  • [15] Ahmed K. T., Sun J., Chen W., Martinez I., Cheng S., Zhang W., Zhang W., In silico model for miRNA-mediated regulatory network in cancer. Brief. Bioinform., 22(6), 2021, 1–13.
  • [16] Sadeghi M., Cava C., Mousavi P., Sabetian S., Insilico-based identification of survival-associated lncRNAs, mRNAs and, miRNAs in breast cancer, Research Square, (2022) 1-21.
  • [17] Kartha R.V., Subramanian S., Competing endogenous RNAs (ceRNAs): new entrants to the intricacies of gene regulation, Front Genet., 5 (8) (2014) 1-9.
  • [18] Akkaya Z.Y., Dinçer P., The new era in therapeutic approaches: Non-coding RNAs and diseases, Marmara Medical Journal, 26 (1) (2013) 5-10.
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  • [20] Ebert M.S., Neilson J.R., Sharp P.A., MicroRNA sponges: Competitive inhibitors of small RNAs in mammalian cells, Nat. Methods, 4 (9) (2007) 721–726.
  • [21] Arvey A., Larsson E., Sander C., Leslie C.S., Marks D.S., Target mRNA abundance dilutes microRNA and siRNA activity. Mol. Syst. Biol., 6 (1) (2010) 1-7.
  • [22] Ebert M.S., Sharp P.A., Emerging Roles for Natural MicroRNA Sponges, Curr. Biol., 20 (19) (2010) R858–R861.
  • [23] Sen R., Ghosal S., Das S., Balti S., Chakrabarti J., Competing endogenous RNA: the key to posttranscriptional regulation. Sci. World J., 2014 (896206) (2014) 1-7.
  • [24] Wu D., Zhu J., Fu Y., Li C., Wu B., LncRNA HOTAIR promotes breast cancer progression through regulating the miR-129-5p/FZD7 axis. Cancer Biomarkers, 30(2) (2021) 203–212.
  • [25] Misir S., Hepokur C., Aliyazicioglu Y., Enguita F. J., Biomarker potentials of miRNA-associated circRNAs in breast cancer (MCF-7) cells: an in vitro and in silico study, Mol Biol Rep., 48(3) (2021) 2463-2471.
  • [26] Brown T.C., Murtha T.D., Rubinstein J.C., Korah R., Carling T., SLC12A7 alters adrenocortical carcinoma cell adhesion properties to promote an aggressive invasive behavior. Cell Commun Signal.,16(1) (2018) 1-13.
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  • [29] Küper C., Beck F.X., Neuhofer W., NFAT5-mediated expression of S100A4 contributes to proliferation and migration of renal carcinoma cells, Front Physiol.,5 (293) (2014) 1-10.
  • [30] Mishra S.K., Siddique H.R., Saleem M., S100A4 calcium-binding protein is key player in tumor progression and metastasis: preclinical and clinical evidence, Cancer Metastasis Rev., 31 (2012) 163–172.
  • [31] Su J.L., Yen C.J., Chen P.S., Chuang S.E., Hong C.C., Kuo I.H., Chen H.Y., Hung M.C., Kuo M.L., The role of the VEGF-C/VEGFR-3 axis in cancer progression, Br J Cancer. 96 (2007) 541–545.
  • [32] Remo A., Simeone I., Pancione M., Parcesepe P., Finetti P., Cerulo L., Bensmail H., Birnbaum D., Van Laere S.J., Colantuoni V., Bonetti F., Bertucci F., Manfrin E., Ceccarelli M., Systems biology analysis reveals NFAT5 as a novel biomarker and master regulator of inflammatory breast cancer, J. Transl. Med., 13(1) (2015) 1-13.
  • [33] Nayler O., Stamm S., and Ullrich A., Characterization and comparison of four serine- and arginine-rich (SR) protein kinases, Biochem. J., 326 (1997) 693–700.
  • [34] Cesana M., Guo M.H., Cacchiarelli D., Wahlster L., Barragan J., Doulatov S., Vo L.T., Salvatori B., Trapnell C., Clement K., Cahan P., Tsanov K. M., Sousa P.M., Tazon-Vega B., Bolondi A., Giorgi F.M., Califano A., Rinn J.L., Meissner A., Hirschhorn J.N., Daley G. Q., A CLK3-HMGA2 alternative splicing axis impacts human hematopoietic stem cell molecular identity throughout development, Cell Stem Cell., 22 (e7) (2018) 575–588.
  • [35] Bowler E., Porazinski S., Uzor S., Thibault P., Durand M., Lapointe E., Rouschop K.M.A., Hancock J., Wilson I., and Ladomery M., Hypoxia leads to significant changes in alternative splicing and elevated expression of CLK splice factor kinases in PC3 prostate cancer cells, BMC Cancer., 18 (2018) 1-11.

An In Silico Approach to Define Potential Biomarkers of miRNA-Associated ceRNAs for Breast Cancer

Year 2023, , 53 - 61, 26.03.2023

Serap Ozer Yaman , Sema Mısır

https://doi.org/10.17776/csj.1230387

Abstract

Breast cancer (BC) is the most common type of cancer with the highest incidence in women. Particularly in breast cancer, competing endogenous RNAs (ceRNAs) play crucial roles in a variety of metabolic pathways including proliferation, migration, and apoptosis. The aim of the present study is to identify combinatorial target genes (ceRNAs) by employing in silico research to identify miRNAs specific to BC. The other aim was to determine possible biomarkers for the diagnosis of BC by selecting those containing the Transcribed Ultra Conserved Region (T-UCR). Using the miRWalk database, 40 miRNAs that have been experimentally shown to be clinically linked with BC were found. T-UCR-containing genes with potential ceRNA activity were identified. Genes with statistically significant changes in expression between BC and normal breast tissue were identified using the GEPIA. The relationship of the CLK3 and NFAT5 genes was found using the Spearman correlation test. The Spearman correlation test was used to determine the association between the CLK3 and NFAT5 genes, and the genes were found to be significantly less expressed in BC. The NFAT5 and CLK3 gene pair have been found to be associated with BC (p<0.001; r=0.35), and may function as useful biomarkers for BC.

Keywords

Biomarker Breast cancer ceRNA miRNA.

References

  • [1] Ferlay J., Soerjomataram I., Dikshit R., Eser S., Mathers C., Rebelo M., Parkin D.M., Forman D., Bray F., Cancer incidence and mortality worldwide: Sources, methods and major patterns in GLOBOCAN 2012, Int. J. Cancer., 136 (5) (2015) E359–E386.
  • [2] Bray F., Ferlay J., Soerjomataram I., Siegel R.L., Torre L.A., Jemal A., Global cancer statistics 2018:GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries, CA Cancer J Clin.,68(6) (2018) 394-424.
  • [3] Wang L., Early diagnosis of breast cancer, Sensors., 17(7) (2017) 1-20.
  • [4] Loh H. Y., Norman B. P., Lai K. S., Rahman N. M. A. N. A., Alitheen N. B. M., Osman M. A., The regulatory role of microRNAs in breast cancer, Int. J. Mol. Sci., 20(19) (2019) 1-27.
  • [5] Szczepanek J., Skorupa M., Tretyn A., MicroRNA as a potential therapeutic molecule in cancer, Cells, 11(6) (2022) 1-24.
  • [6] Jang J. Y., Kim Y. S., Kang K. N., Kim K. H., Park Y. J., Kim, C. W., Multiple microRNAs as biomarkers for early breast cancer diagnosis, Mol Clin Oncol., 14(2) (2021) 1-9.
  • [7] Qi X., Zhang D.H., Wu N., Xiao J.H., Wang X., Ma W., CeRNA in cancer: possible functions and clinical implications, J Med Genet., 52(10) (2015) 710-8.
  • [8] Fassan M., Dall'Olmo L., Galasso M., Braconi C., Pizzi M., Realdon S., Volinia S., Valeri N., Gasparini P., Baffa R., Souza R.F., Vicentini C., D'Angelo E., Bornschein J., Nuovo G.J., Zaninotto G., Croce C. M., Rugge M., Transcribed ultraconserved noncoding RNAs (TUCR) are involved in Barrett's esophagus carcinogenesis, Oncotarget, 5(16) (2014) 7162-71.
  • [9] Dweep H., Gretz N., miRWalk2. 0: a comprehensive atlas of microRNA-target interactions, Nat Methods., 12 (8) (2015) 697-697.
  • [10] Coronnello C., Benos P.V., ComiR: combinatorial microRNA target prediction tool, Nucleic Acids Res., 41(W1) (2013) W159-W164.
  • [11] Bejerano G., Pheasant M., Makunin I., Stephen S., Kent W.J., Mattick J.S., Haussler D., Ultraconserved elements in the human genome. Science., 304(5675) (2004) 1321-5.
  • [12] Tang Z., Li C., Kang B., GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses, Nucleic Acids Res., 45(W1) (2017) W98-W102
  • [13] Ghoncheh M., Pournamdar Z., Salehiniya H., Incidence and mortality and epidemiology of breast cancer in the world. Asian Pac. J. Cancer Prev, 17(sup3) (2016) 43-46.
  • [14] Bettaieb A., Paul C., Plenchette S., Shan J., Chouchane L., Ghiringhelli F., Precision Medicine in Breast Cancer: Reality or Utopia? J Transl Med, 15 (1) (2017) 1-13.
  • [15] Ahmed K. T., Sun J., Chen W., Martinez I., Cheng S., Zhang W., Zhang W., In silico model for miRNA-mediated regulatory network in cancer. Brief. Bioinform., 22(6), 2021, 1–13.
  • [16] Sadeghi M., Cava C., Mousavi P., Sabetian S., Insilico-based identification of survival-associated lncRNAs, mRNAs and, miRNAs in breast cancer, Research Square, (2022) 1-21.
  • [17] Kartha R.V., Subramanian S., Competing endogenous RNAs (ceRNAs): new entrants to the intricacies of gene regulation, Front Genet., 5 (8) (2014) 1-9.
  • [18] Akkaya Z.Y., Dinçer P., The new era in therapeutic approaches: Non-coding RNAs and diseases, Marmara Medical Journal, 26 (1) (2013) 5-10.
  • [19] Salmena L., Poliseno L., Tay Y., Kats L., Pandolfi P.P., A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language? Cell, 146 (3) (2011) 353–358.
  • [20] Ebert M.S., Neilson J.R., Sharp P.A., MicroRNA sponges: Competitive inhibitors of small RNAs in mammalian cells, Nat. Methods, 4 (9) (2007) 721–726.
  • [21] Arvey A., Larsson E., Sander C., Leslie C.S., Marks D.S., Target mRNA abundance dilutes microRNA and siRNA activity. Mol. Syst. Biol., 6 (1) (2010) 1-7.
  • [22] Ebert M.S., Sharp P.A., Emerging Roles for Natural MicroRNA Sponges, Curr. Biol., 20 (19) (2010) R858–R861.
  • [23] Sen R., Ghosal S., Das S., Balti S., Chakrabarti J., Competing endogenous RNA: the key to posttranscriptional regulation. Sci. World J., 2014 (896206) (2014) 1-7.
  • [24] Wu D., Zhu J., Fu Y., Li C., Wu B., LncRNA HOTAIR promotes breast cancer progression through regulating the miR-129-5p/FZD7 axis. Cancer Biomarkers, 30(2) (2021) 203–212.
  • [25] Misir S., Hepokur C., Aliyazicioglu Y., Enguita F. J., Biomarker potentials of miRNA-associated circRNAs in breast cancer (MCF-7) cells: an in vitro and in silico study, Mol Biol Rep., 48(3) (2021) 2463-2471.
  • [26] Brown T.C., Murtha T.D., Rubinstein J.C., Korah R., Carling T., SLC12A7 alters adrenocortical carcinoma cell adhesion properties to promote an aggressive invasive behavior. Cell Commun Signal.,16(1) (2018) 1-13.
  • [27] Burg M.B., Ferraris J.D., Dmitrieva N.I., Cellular response to hyperosmotic stresses. Physiol Rev., 87(4) (2007) 1441-1474.
  • [28] Chen M., Sastry S.K., O’Connor K.L., Src kinase pathway is involved in NFAT5-mediated S100A4 induction by hyperosmotic stress in colon cancer cells, Am J Physiol Cell Physiol., 300(5) (2011) C1155-C1163.
  • [29] Küper C., Beck F.X., Neuhofer W., NFAT5-mediated expression of S100A4 contributes to proliferation and migration of renal carcinoma cells, Front Physiol.,5 (293) (2014) 1-10.
  • [30] Mishra S.K., Siddique H.R., Saleem M., S100A4 calcium-binding protein is key player in tumor progression and metastasis: preclinical and clinical evidence, Cancer Metastasis Rev., 31 (2012) 163–172.
  • [31] Su J.L., Yen C.J., Chen P.S., Chuang S.E., Hong C.C., Kuo I.H., Chen H.Y., Hung M.C., Kuo M.L., The role of the VEGF-C/VEGFR-3 axis in cancer progression, Br J Cancer. 96 (2007) 541–545.
  • [32] Remo A., Simeone I., Pancione M., Parcesepe P., Finetti P., Cerulo L., Bensmail H., Birnbaum D., Van Laere S.J., Colantuoni V., Bonetti F., Bertucci F., Manfrin E., Ceccarelli M., Systems biology analysis reveals NFAT5 as a novel biomarker and master regulator of inflammatory breast cancer, J. Transl. Med., 13(1) (2015) 1-13.
  • [33] Nayler O., Stamm S., and Ullrich A., Characterization and comparison of four serine- and arginine-rich (SR) protein kinases, Biochem. J., 326 (1997) 693–700.
  • [34] Cesana M., Guo M.H., Cacchiarelli D., Wahlster L., Barragan J., Doulatov S., Vo L.T., Salvatori B., Trapnell C., Clement K., Cahan P., Tsanov K. M., Sousa P.M., Tazon-Vega B., Bolondi A., Giorgi F.M., Califano A., Rinn J.L., Meissner A., Hirschhorn J.N., Daley G. Q., A CLK3-HMGA2 alternative splicing axis impacts human hematopoietic stem cell molecular identity throughout development, Cell Stem Cell., 22 (e7) (2018) 575–588.
  • [35] Bowler E., Porazinski S., Uzor S., Thibault P., Durand M., Lapointe E., Rouschop K.M.A., Hancock J., Wilson I., and Ladomery M., Hypoxia leads to significant changes in alternative splicing and elevated expression of CLK splice factor kinases in PC3 prostate cancer cells, BMC Cancer., 18 (2018) 1-11.
There are 35 citations in total.

Details

Primary Language English
Subjects Genetics
Journal Section Natural Sciences
Authors

Serap Ozer Yaman 0000-0002-5089-0836

Sema Mısır 0000-0002-5919-3295

Publication Date March 26, 2023
Submission Date January 6, 2023
Acceptance Date March 17, 2023
Published in Issue Year 2023

Cite

APA Ozer Yaman, S., & Mısır, S. (2023). An In Silico Approach to Define Potential Biomarkers of miRNA-Associated ceRNAs for Breast Cancer. Cumhuriyet Science Journal, 44(1), 53-61. https://doi.org/10.17776/csj.1230387