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Plant Science Today (PST)

Research Articles

Vol. 12 No. 1 (2025)

A systems biology-based study to assess the effects of TNF-alpha ± apigenin in triple-negative breast cancer cell line

DOI
https://doi.org/10.14719/pst.3566
Submitted
15 June 2024
Published
23-12-2024 — Updated on 01-01-2025
Versions

Abstract

Triple-negative breast cancer (TNBC) is a type of breast cancer that lacks estrogen, progesterone, and HER2 receptors. Various treatment methods are available for breast cancer, but therapies with minimal toxic side effects are particularly important. This study  computationally investigates the impact of apigenin, a compound used in traditional Chinese medicine, on the TNBC cell line. The GSE120550 dataset was retrieved from the NCBI-GEO database. BRB-ArrayTools were used for pre- and post-processing to identify significantly differentially expressed genes. Additionally, the DAVID web server was utilized to analyze three main components: "biological process," "cellular component," and "molecular function," along with the KEGG signaling pathway. Finally, a Venn diagram was employed to thoroughly investigate the number of shared genes among 15 groups derived from 6 compared sample sets. The primary analysis of 6 pairs of samples revealed significant differentially expressed genes (DEGs), which were prioritized using the TOPPgene web server. These identified genes, playing key roles in inhibiting the progression of BC, are involved in various signaling pathways. Protein-protein interaction network analysis highlighted the biomarkers associated with the inhibitory effects of apigenin across the 15 sets derived from the 6 sample pairs. The findings of this study confirm the inhibitory effects of apigenin, with no toxic side effects, on patients with TNBC. This natural compound holds promise for future therapeutics and novel drug designs.

References

  1. Pérez-García J, Soberino J, Racca F, Gion M, Stradella A, Cortés J. Atezolizumab in the treatment of metastatic triple-negative breast cancer. Expert Opin Biol Ther. 2020;1-9. https://doi.org/10.1080/14712598.2020.1769063
  2. He J, Peng T, Peng Y, Ai L, Deng Z, Wang X-Q, et al. Molecularly engineering triptolide with aptamers for high specificity and cytotoxicity for triple-negative breast cancer. J Am Chem Soc. 2020;142(6):2699-703. https://doi.org/10.1021/jacs.9b10510
  3. Cleator S, Heller W, Coombes RC. Triple-negative breast cancer: Therapeutic options. The Lancet Oncology. 2007;8(3):235-44. https://doi.org/10.1016/S1470-2045(07)70074-8
  4. Hulamani S, Durgannavar NA. Triple negative breast cancer (TNBC). In: Rajenderan R, Mishra Sakun, Vhanalakar A, editors. Advances in and Humanities Research; 2020: p. 8-16.
  5. Cruceriu D, Baldasici O, Balacescu O, Berindan-Neagoe I. The dual role of tumor necrosis factor-alpha (TNF-alpha) in breast cancer: Molecular insights and therapeutic approaches. Cell Oncol. 2020;43(1):1-18. https://doi.org/10.1007/s13402-019-00489-1
  6. Mahdavi Sharif P, Jabbari P, Razi S, Keshavarz-Fathi M, Rezaei N. Importance of TNF-alpha and its alterations in the development of cancers. Cytokine. 2020;130:155066. https://doi.org/10.1016/j.cyto.2020.155066
  7. Tao X, Lipsky PE. The chinese anti-inflammatory and immunosuppressive herbal remedy Tripterygium wilfordii Hook f. Rheumatic Disease Clinics of North America. 2000;26(1):29-50. https://doi.org/10.1016/s0889-857x(05)70118-6
  8. Wang J, Yang X, Han H, Wang L, Bao W, Wang S, et al. Inhibition of growth and metastasis of triple-negative breast cancer targeted by traditional chinese medicine tubeimu in orthotopic mice models. Chinese Journal of Cancer Research = Chung-Kuo Yen Cheng Yen Chiu. 2018;30(1):112-21. https://doi.org/10.21147/j.issn.1000-9604.2018.01.12
  9. Marshall ML, Fung KY, Jans DA, Wagstaff KM. Tumour-specific phosphorylation of serine 419 drives alpha-enolase (ENO1) nuclear export in triple negative breast cancer progression. Cell Biosci. 2024;14(1):74. https://doi.org/10.1186/s13578-024-01249-x
  10. Won KA, Spruck C. Triple negative breast cancer therapy: Current and future perspectives (Review). Int J Oncol. 2020;57(6):1245-61. https://doi.org/10.3892/ijo.2020.5135
  11. Su YY, Liu YL, Huang HC, Lin CC. Ensemble learning model for identifying the hallmark genes of NFkappaB/TNF signaling pathway in cancers. J Transl Med. 2023;21(1):485. https://doi.org/10.1186/s12967-023-04355-5
  12. Bauer D, Mazzio E, Soliman KFA. Whole transcriptomic analysis of apigenin on TNF alpha immuno-activated MDA-MB-231 breast cancer cells. Cancer Genomics and Proteomics. 2019;16(6):421-32. https://doi.org/10.21873/cgp.20146
  13. Bauer D, Mazzio E, Hilliard A, Oriaku ET, Soliman KFA. Effect of apigenin on whole transcriptome profile of TNFalpha-activated MDA-MB-468 triple negative breast cancer cells. Oncol Lett. 2020;19(3):2123-32. https://doi.org/10.3892/ol.2020.11327
  14. Lee HH, Jung J, Moon A, Kang H, Cho H. Antitumor and anti-invasive effect of apigenin on human breast carcinoma through suppression of IL-6 expression. Int J Mol Sci. 2019;20(13):3143. https://doi.org/10.3390%2Fijms20133143
  15. Kabala-Dzik A, Rzepecka-Stojko A, Kubina R, Iriti M, Wojtyczka RD, Buszman E, et al. Flavonoids, bioactive components of propolis, exhibit cytotoxic activity and induce cell cycle arrest and apoptosis in human breast cancer cells MDA-MB-231 and MCF-7 – A comparative study. Cellular and Molecular Biology. 2018;64(8):1-10. https://dx.doi.org/10.14715/cmb/2018.64.8.1
  16. Lee HH, Cho H. Anti-cancer effect of apigenin on human breast carcinoma MDA-MB-231 through cell cycle arrest and apoptosis. Microbiology and Biotechnology Letters. 2019;47(1):34-42. https://doi.org/10.3390/ijms25105569
  17. Golonko A, Olichwier AJ, Szklaruk A, Paszko A, Swislocka R, Szczerbinski L, et al. Apigenin's modulation of doxorubicin efficacy in breast cancer. Molecules. 2024;29(11):2603. https://doi.org/10.3390/molecules29112603
  18. Madunic J, Madunic IV, Gajski G, Popic J, Garaj-Vrhovac V. Apigenin: A dietary flavonoid with diverse anti-cancer properties. Cancer Lett. 2018;413:11-22. https://doi.org/10.1016/j.canlet.2017.10.041
  19. Sung B, Chung HY, Kim ND. Role of apigenin in cancer prevention via the induction of apoptosis and autophagy. Journal of Cancer Prevention. 2016;21(4):216. https://doi.org/10.15430/jcp.2016.21.4.216
  20. Park C-H, Min S-Y, Yu H-W, Kim K, Kim S, Lee H-J, et al. Effects of apigenin on RBL-2H3, RAW264.7 and HaCaT cells: Anti-allergic, anti-inflammatory and skin-protective activities. Int J Mol Sci. 2020;21(13):4620. https://doi.org/10.3390/ijms21134620
  21. Wang M, Firrman J, Liu L, Yam K. A review on flavonoid apigenin: Dietary intake, ADME, antimicrobial effects and interactions with human gut microbiota. BioMed Research International. 2019;2019. https://doi.org/10.1155/2019/7010467
  22. Wang W, Yue RF, Jin Z, He LM, Shen R, Du D, et al. Efficiency comparison of apigenin-7-O-glucoside and trolox in antioxidative stress and anti-inflammatory properties. J Pharm Pharmacol. 2020. https://doi.org/10.1111/jphp.13347
  23. Tong X, Pelling JC. Targeting the PI3K/Akt/mTOR axis by apigenin for cancer prevention. Anti-cancer Agents Med Chem. 2013;13(7):971-78. https://doi.org/10.2174/18715206113139990119
  24. Xu M, Wang S, Song Y, Yao J, Huang K, Zhu X. Apigenin suppresses colorectal cancer cell proliferation, migration and invasion via inhibition of the Wnt/beta-catenin signaling pathway. Oncol Lett. 2016;11(5):3075-80. https://doi.org/10.3892/ol.2016.4331
  25. Cao H-H, Chu J-H, Kwan H-Y, Su T, Yu H, Cheng C-Y, et al. Inhibition of the STAT3 signaling pathway contributes to apigenin-mediated anti-metastatic effect in melanoma. Sci Rep. 2016;6(1):1-12. https://doi.org/10.1038/srep21731
  26. Melaibari M, Alkreathy HM, Esmat A, Rajeh NA, Shaik RA, Alghamdi AA, et al. Anti-fibrotic efficacy of apigenin in a mice model of carbon tetrachloride-induced hepatic fibrosis by modulation of oxidative stress, inflammation and fibrogenesis: A preclinical study. Biomedicines. 2023;11(5):1342. https://doi.org/10.3390/biomedicines11051342
  27. Mendonca P, Alghamdi S, Messeha S, Soliman KFA. Pentagalloyl glucose inhibits TNF-alpha-activated CXCL1/GRO-alpha expression and induces apoptosis-related genes in triple-negative breast cancer cells. Sci Rep. 2021;11(1):5649. https://doi.org/10.1038/s41598-021-85090-z
  28. Ahmed SA, Mendonca P, Messeha SS, Oriaku ET, Soliman KFA. The anti-cancer effects of marine carotenoid fucoxanthin through phosphatidylinositol 3-kinase (PI3K)-AKT signaling on triple-negative breast cancer cells. Molecules. 2023;29(1):61. https://doi.org/10.3390/molecules29010061
  29. Truong VN, Nguyen YT, Cho SK. Ampelopsin suppresses stem cell properties accompanied by attenuation of oxidative phosphorylation in chemo- and radio-resistant MDA-MB-231 breast cancer cells. Pharmaceuticals (Basel). 2021;14(8):794. https://doi.org/10.3390/ph14080794
  30. Jin H, Ko YS, Kim HJ. P2Y2R-mediated inflammasome activation is involved in tumor progression in breast cancer cells and in radiotherapy-resistant breast cancer. Int J Oncol. 2018;53(5):1953-66. https://doi.org/10.3892/ijo.2018.4552
  31. Amjad E, Asnaashari S, Sokouti B, Dastmalchi S. Systems biology comprehensive analysis on breast cancer for identification of key gene modules and genes associated with TNM-based clinical stages. Sci Rep. 2020;10(1):10816. https://doi.org/10.1038/s41598-020-67643-w
  32. Amjad E, Asnaashari S, Sokouti B, Dastmalchi S. Impact of gene biomarker discovery tools based on protein–protein interaction and machine learning on performance of artificial intelligence models in predicting clinical stages of breast cancer. Interdisciplinary Sciences: Computational Life Sciences. 2020. https://doi.org/10.1007/s12539-020-00390-8
  33. Carvalho B. pd.hugene.1.0.st.v1: Platform Design Info for Affymetrix HuGene-1_0-st-v1. R package. 2015. https://www.bioconductor.org/packages/release/data/annotation/html/pd.hugene.1.0.st.v1.html
  34. Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44-57. https://doi.org/10.1038/nprot.2008.211
  35. Huang da W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009;37(1):1-13. https://doi.org/10.1093/nar/gkn923
  36. Zhou G, Soufan O, Ewald J, Hancock REW, Basu N, Xia J. NetworkAnalyst 3.0: A visual analytics platform for comprehensive gene expression profiling and meta-analysis. NAR. 2019;47(W1):W234-W41. https://doi.org/10.1093/nar/gkz240
  37. Xia J, Gill EE, Hancock REW. Network analyst for statistical, visual and network-based meta-analysis of gene expression data. Nat Protoc. 2015;10(6):823-44. https://doi.org/10.1038/nprot.2015.052
  38. Oliveros J. 2007–2015. Venny. An interactive tool for comparing lists with Venn’s diagrams. 2017. https://bioinfogp.cnb.csic.es/tools/venny/
  39. Tseng TH, Chien MH, Lin WL, Wen YC, Chow JM, Chen CK, et al. Inhibition of MDA-MB-231 breast cancer cell proliferation and tumor growth by apigenin through induction of G2/M arrest and histone H3 acetylation-mediated p21(WAF1/CIP1) expression. Environmental Toxicology. 2017;32(2):434-44. https://doi.org/10.1002/tox.22247
  40. Nabavi SM, Habtemariam S, Daglia M, Nabavi SF. Apigenin and breast cancers: From chemistry to medicine. Anti-Cancer Agents in Medicinal Chemistry. 2015;15(6):728-35. https://doi.org/10.2174/1871520615666150304120643
  41. Huang C, Wei YX, Shen MC, Tu YH, Wang CC, Huang HC. Chrysin, abundant in Morinda citrifolia fruit water-EtOAc extracts, combined with apigenin synergistically induced apoptosis and inhibited migration in human breast and liver cancer cells. Journal of Agricultural and Food Chemistry. 2016;64(21):4235-45. https://doi.org/10.1021/acs.jafc.6b00766
  42. Evani SJ, Prabhu RG, Gnanaruban V, Finol EA, Ramasubramanian AK. Monocytes mediate metastatic breast tumor cell adhesion to endothelium under flow. FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology. 2013;27(8):3017-29. https://doi.org/10.1096%2Ffj.12-224824
  43. Montemagno C, Dumas L, Cavailles P, Ahmadi M, Bacot S, Debiossat M, et al. In vivo assessment of VCAM-1 expression by SPECT/CT imaging in mice models of human triple negative breast cancer. Cancers (Basel). 2019;11(7):1039. https://doi.org/10.3390/cancers11071039
  44. Hong OY, Jang HY, Lee YR, Jung SH, Youn HJ, Kim JS. Inhibition of cell invasion and migration by targeting matrix metalloproteinase-9 expression via sirtuin 6 silencing in human breast cancer cells. Sci Rep. 2022;12(1):12125. https://doi.org/10.1038/s41598-022-16405-x
  45. Zhao X, Sun X, Gao F, Luo J, Sun Z. Effects of ulinastatin and docataxel on breast tumor growth and expression of IL-6, IL-8, and TNF-alpha. Journal of Experimental and Clinical Cancer Research. 2011;30(1):22. https://doi.org/10.1186/1756-9966-30-22
  46. Choi YK, Cho SG, Woo SM, Yun YJ, Jo J, Kim W, et al. Saussurea lappa Clarke-derived costunolide prevents TNF alpha- induced breast cancer cell migration and invasion by inhibiting NF- kB activity. Evidence-Based Complementary and Alternative Medicine : eCAM. 2013;2013:936257. https://doi.org/10.1155/2013/936257
  47. Lee J, Hahm ER, Marcus AI, Singh SV. Withaferin A inhibits experimental epithelial-mesenchymal transition in MCF-10A cells and suppresses vimentin protein level in vivo in breast tumors. Molecular Carcinogenesis. 2015;54(6):417-29. https://doi.org/10.1002%2Fmc.22110
  48. El Hasasna H, Saleh A, Al Samri H, Athamneh K, Attoub S, Arafat K, et al. Rhus coriaria suppresses angiogenesis, metastasis and tumor growth of breast cancer through inhibition of STAT3, NFkB and nitric oxide pathways. Sci Rep. 2016;6:21144. https://doi.org/10.1038/srep21144
  49. Geng Y, Chandrasekaran S, Hsu JW, Gidwani M, Hughes AD, King MR. Phenotypic switch in blood: Effects of pro-inflammatory cytokines on breast cancer cell aggregation and adhesion. PloS One. 2013;8(1):e54959. https://doi.org/10.1371%2Fjournal.pone.0054959
  50. Thomas R, Al-Rashed F, Akhter N, Al-Mulla F, Ahmad R. ACSL1 regulates TNF alpha-induced GM-CSF production by breast cancer MDA-MB-231 cells. Biomolecules. 2019;9(10):555. https://doi.org/10.3390/biom9100555
  51. Mungrue K, Ramdath J, Ali S, Cuffie WA, Dodough N, Gangar M, et al. Challenges to the control of breast cancer in a small developing country. Breast Cancer: Basic and Clinical Research. 2014;8(1):7-13. https://doi.org/10.4137/bcbcr.s12780
  52. Feng XY, Lu S, Hao XS, Liu H. Breast cancer screening: Review of history and current status in western developed countries. Tumor. 2015;35(4):453-60 and 66. http://dx.doi.org/10.3781/j.issn.1000-7431.2015.55.746
  53. Song YK, Yoon JH, Woo JK, Kang JH, Lee KR, Oh SH, et al. Quercetin is a flavonoid breast cancer resistance protein inhibitor with an impact on the oral pharmacokinetics of sulfasalazine in rats. Pharmaceutics. 2020;12(5). https://doi.org/10.3390/pharmaceutics12050397
  54. Goodarzi S, Tabatabaei MJ, Mohammad Jafari R, Shemirani F, Tavakoli S, Mofasseri M, et al. Cuminum cyminum fruits as source of luteolin- 7-O-glucoside, potent cytotoxic flavonoid against breast cancer cell lines. Nat Prod Res. 2020;34(11):1602-06. https://doi.org/10.1080/14786419.2018.1519824
  55. Ko YC, Choi HS, Liu R, Kim JH, Kim SL, Yun BS, et al. Inhibitory effects of tangeretin, a citrus peel-derived flavonoid, on breast cancer stem cell formation through suppression of Stat3 signaling. Molecules (Basel, Switzerland). 2020;25(11). https://doi.org/10.3390/molecules25112599
  56. Abd Razik BA, Ezzat MO, Al-Shohani ADH. Molecular docking and design study for anti-cancer activity of flavonoid derivatives against breast cancer. Indian Drugs. 2020;57(4):7-14. http://doi.org/10.53879/id.57.04.12202
  57. Hong J, Fristiohady A, Nguyen CH, Milovanovic D, Huttary N, Krieger S, et al. Apigenin and luteolin attenuate the breaching of MDA-MB231 breast cancer spheroids through the lymph endothelial barrier in vitro. Front Pharmacol. 2018;9(MAR). https://doi.org/10.3389/fphar.2018.00220
  58. Bauer D, Redmon N, Mazzio E, Soliman KF. Apigenin inhibits TNF alpha/IL-1 alpha-induced CCL2 release through IKBK-epsilon signaling in MDA-MB-231 human breast cancer cells. PLoS One. 2017;12(4). https://doi.org/10.1371/journal.pone.0175558
  59. Lee WJ, Chen WK, Wang CJ, Lin WL, Tseng TH. Apigenin inhibits HGF-promoted invasive growth and metastasis involving blocking PI3K/Akt pathway and beta 4 integrin function in MDA-MB-231 breast cancer cells. Toxicol Appl Pharmacol. 2008;226(2):178-91. https://doi.org/10.1016/j.taap.2007.09.013
  60. Nandy D, Rajam SM, Dutta D. A three layered histone epigenetics in breast cancer metastasis. Cell Biosci. 2020;10:1-23. https://doi.org/10.1186/s13578-020-00415-1
  61. Long M, Sun X, Shi W, Yanru A, Leung ST, Ding D, et al. A novel histone H4 variant H4G regulates rDNA transcription in breast cancer. NAR. 2019;47(16):8399-409. https://doi.org/10.1093/nar/gkz547
  62. Prieto-Dominguez N, Parnell C, Teng Y. Drugging the small GTPase pathways in cancer treatment: Promises and challenges. Cells. 2019;8(3):255. https://doi.org/10.3390/cells8030255
  63. Haga RB, Ridley AJ. Rho GTPases: Regulation and roles in cancer cell biology. Small GTPases. 2016;7(4):207-21. https://doi.org/10.1080%2F21541248.2016.1232583
  64. Tan J, Yu C-Y, Wang Z-H, Chen H-Y, Guan J, Chen Y-X, et al. Genetic variants in the inositol phosphate metabolism pathway and risk of different types of cancer. Sci Rep. 2015;5:8473. https://doi.org/10.1038/srep08473
  65. Hernandez-Aya LF, Gonzalez-Angulo AM. Targeting the phosphatidylinositol 3-kinase signaling pathway in breast cancer. The Oncologist. 2011;16(4):404-14. https://doi.org/10.1634/theoncologist.2010-0402
  66. Miller TW, Rexer BN, Garrett JT, Arteaga CL. Mutations in the phosphatidylinositol 3-kinase pathway: Role in tumor progression and therapeutic implications in breast cancer. Breast Cancer Research: BCR. 2011;13(6):224. https://doi.org/10.1186/bcr3039
  67. Fry MJ. Phosphoinositide 3-kinase signalling in breast cancer: How big a role might it play? Breast Cancer Res. 2001;3(5):304. https://doi.org/10.1186/bcr312
  68. Farman FU, Haq F, Muhammad N, Ali N, Rahman H, Saeed M. Aberrant promoter methylation status is associated with upregulation of the E2F4 gene in breast cancer. Oncol Lett. 2018;15(6):8461-69. https://doi.org/10.3892/ol.2018.8382
  69. Simon JW. The association of Herpes simplex virus and cervical cancer: A review. Gynecol Oncol. 1976;4(1):108-16. https://doi.org/10.1016/0090-8258(76)90011-1
  70. Li M, Guo Y, Feng Y-M, Zhang N. Identification of triple-negative breast cancer genes and a novel high-risk breast cancer prediction model development based on PPI data and support vector machines. Frontiers in Genetics. 2019;10(180). https://doi.org/ 10.3389/fgene.2019.00180
  71. Wang W, Nag SA, Zhang R. Targeting the NFkB signaling pathways for breast cancer prevention and therapy. Curr Med Chem. 2015;22(2):264-89. https://doi.org/ 10.2174/0929867321666141106124315
  72. Smith SM, Lyu YL, Cai L. NF-kB affects proliferation and invasiveness of breast cancer cells by regulating CD44 expression. PLoS One. 2014;9(9):e106966. https://doi.org/ 10.1371/journal.pone.0106966

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