اخبار و اعلانات

 آمار

تعداد نشریات282
تعداد نشریات سازمان80
تعداد شماره‌ها3,219
تعداد مقالات35,690
تعداد مشاهده مقاله53,566,333
تعداد دریافت فایل اصل مقاله92,845,264
Dini, Salome, Ghorbani, Abozar, Eskandarzade, Neda, Alibeiki, Maryam. (1405). A Bioinformatics Approach to Predict Long non-coding RNA Targets of Shikonin in Apoptosis Induction of Breast Cancer Cells. سامانه مدیریت نشریات علمی, 15(5), 614-620. doi: 10.22034/jmpb.2026.371148.2081
Salome Dini; Abozar Ghorbani; Neda Eskandarzade; Maryam Alibeiki. "A Bioinformatics Approach to Predict Long non-coding RNA Targets of Shikonin in Apoptosis Induction of Breast Cancer Cells". سامانه مدیریت نشریات علمی, 15, 5, 1405, 614-620. doi: 10.22034/jmpb.2026.371148.2081
Dini, Salome, Ghorbani, Abozar, Eskandarzade, Neda, Alibeiki, Maryam. (1405). 'A Bioinformatics Approach to Predict Long non-coding RNA Targets of Shikonin in Apoptosis Induction of Breast Cancer Cells', سامانه مدیریت نشریات علمی, 15(5), pp. 614-620. doi: 10.22034/jmpb.2026.371148.2081
Dini, Salome, Ghorbani, Abozar, Eskandarzade, Neda, Alibeiki, Maryam. A Bioinformatics Approach to Predict Long non-coding RNA Targets of Shikonin in Apoptosis Induction of Breast Cancer Cells. سامانه مدیریت نشریات علمی, 1405; 15(5): 614-620. doi: 10.22034/jmpb.2026.371148.2081

A Bioinformatics Approach to Predict Long non-coding RNA Targets of Shikonin in Apoptosis Induction of Breast Cancer Cells

Journal of Medicinal plants and By-products
مقاله 9، دوره 15، شماره 5، آذر و دی 2026، صفحه 614-620    اصل مقاله (1.37 M)
نوع مقاله: Research Article
شناسه دیجیتال (DOI): 10.22034/jmpb.2026.371148.2081
نویسندگان
Salome Dini* 1؛ Abozar Ghorbani2؛ Neda Eskandarzade3؛ Maryam Alibeiki4
1Young and Elite Researchers Club, Karaj Branch, Islamic Azad University, Karaj, Iran
2Department of Plant Protection, Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj, Iran
3Department of Basic Sciences, School of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
4Department of Microbiology, Faculty of Basic Sciences, Shahrood Branch, Islamic Azad University, Shahrood, Iran
چکیده
Phytochemicals such as shikonin accomplish their pleiotropic anti-tumor activities by modulating the expression of non-coding RNAs. The role of shikonin in modulating long non-coding RNAs (lncRNAs) to induce apoptosis in vitro in breast cancer cells was investigated. An RNA-Seq dataset available in NCBI, in which shikonin induced apoptosis in different breast cancer cell lines, was analysed to examine lncRNA expression. We identified 88 differentially expressed lncRNAs in the shikonin-treated groups. After identifying the 10 up- and down-regulated lncRNAs, we found that dysregulation of putative lncRNAs is associated with cancer pathophysiology, particularly breast cancer. The significantly up- and down-regulated lncRNAs in shikonin-treated cell lines were NEAT1, ALDH1A3-AS1-201, MIR3142HG, AC079305.1, and DDR1-AS1. Furthermore, a network of interactions between key lncRNAs and miRNAs was constructed. Our comparative analysis of the lncRNA transcriptional landscape identified several novel lncRNA candidates that may regulate breast cancer cells' response to shikonin treatment. This may pave the way for the development of new molecular biomarkers with diagnostic, prognostic, and potentially therapeutic applications.
کلیدواژه‌ها
Apoptosis؛ LncRNAs-miRNAs network؛ Shikonin؛ Breast Cancer؛ Phytochemicals
مراجع
  1. Mattick J.S., Amaral P.P., Carninci P., Carpenter S., Chang H.Y., Chen L-L., et al. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nature Reviews Molecular Cell Biology. 2023;1–17.
  2. Fakeri M., Koulaeizadeh S., Armandzadeh S.M., Aboutalebi V., Beilankouhi E., Valilo M., et al. Involvement of miRNA-337 in various cancers. Current Cancer Therapy Reviews. 2024;20:188–199.
  3. Suleiman A.A., Al-Chalabi R., Shaban S.A. Integrative role of small non-coding RNAs in viral immune response: a systematic review. Molecular Biology Reports. 2024;51:107.
  4. Yin R., Lu H., Cao Y., Zhang J., Liu G., Guo Q., et al. The mechanisms of miRNAs on target regulation and their recent advances in atherosclerosis. Current Medicinal Chemistry. 2024;31(35):5779–5804.
  5. Liu Y., Yang P., Wang J., Peng W., Zhao J., Wang Z. miRNA regulates ferroptosis in cardiovascular and cerebrovascular diseases. DNA and Cell Biology. 2024;43(10):492–509.
  6. Manjili D.A., Babaei F.N., Younesirad T., Ghadir S., Askari H., Daraei A. Dysregulated circular RNA- and long non-coding RNA-mediated competing endogenous RNA networks in ovarian and cervical cancers. Archives of Biochemistry and Biophysics. 2025;110389.
  7. Connerty P., Lock R.B., De Bock C.E. Long non-coding RNAs: major regulators of cell stress in cancer. Frontiers in Oncology. 2020;10:285.
  8. Nemeth K., Bayraktar R., Ferracin M., Calin G.A. Non-coding RNAs in disease: from mechanisms to therapeutics. Nature Reviews Genetics. 2024;25(3):211–232.
  9. Kim J., Harper A., McCormack V., Sung H., Houssami N., Morgan E., et al. Global patterns and trends in breast cancer incidence and mortality across 185 countries. Nature Medicine. 2025;1–9.
  10. Ensenyat-Mendez M., Llinàs-Arias P., Orozco J.I.J., Íñiguez-Muñoz S., Salomon M.P., Sesé B., et al. Current triple-negative breast cancer subtypes. Frontiers in Oncology. 2021;11:681476.
  11. Li S., So T., Tang G., Tan H-Y., Wang N., Ng B.F.L., et al. Chinese herbal medicine for reducing chemotherapy-associated side-effects in breast cancer patients. Frontiers in Oncology. 2020;10:599073.
  12. Faruk M. Breast cancer resistance to chemotherapy: when should we suspect it and how can we prevent it? Annals of Medicine and Surgery. 2021;70:102793.
  13. Long F., Li X., Pan J., Ye H., Di C., Huang Y., et al. The role of lncRNA NEAT1 in human cancer chemoresistance. Cancer Cell International. 2024;24(1):236.
  14. Dini S., Chen Q., Fatemi F., Asri Y. Phytochemical and biological activities of some Iranian medicinal plants. Pharmaceutical Biology. 2022;60(1):664–689.
  15. Faezeh F., Dini S., Abolfazl D., Reza Z.M. Antibacterial activity of Zataria multiflora essential oil treated with gamma irradiation. Radiation Physics and Chemistry. 2015;106:145–150.
  16. Dini S., Dadkhah A., Fatemi F. Biological properties of Iranian Zataria multiflora essential oils. Electronic Journal of Biology. 2015;11(3):57–62.
  17. Irandoust F., Dini S. A new perspective of aroma face masks during the COVID-19 pandemic. Journal of Medical Engineering and Technology. 2022;46(3):198–208.
  18. Malayeri M.R.M., Dadkhah A., Fatemi F., Dini S., Torabi F., Tavajjoh M.M., et al. Chemotherapeutic effect of Berberis integerrima extract on colon cancer. Zeitschrift für Naturforschung C. 2016;71(7–8):225–232.
  19. Torabi F., Dadkhah A., Fatemi F., Dini S., Taghizadeh M., Malayeri M.R.M. Prevention and therapy of DMH-induced colon carcinogenesis by Ferula assa-foetida. Turkish Journal of Biochemistry. 2015;40(5):390–400.
  20. Fatemi F., Dadkhah A., Akbarzadeh K., Dini S., Hatami S., Rasooli A. Hepatoprotective effects of deuterium-depleted water with Satureja rechingeri essential oil. Electronic Journal of Biology. 2015;11(2):23–32.
  21. Iranzadeh S., Dalil D., Kohansal S., Isakhani M. Shikonin in breast cancer treatment. Journal of Pharmacy and Pharmacology. 2024;76(8):967–982.
  22. Biswal S., Sahoo S.K., Biswal B.K. Shikonin as a potent phytotherapeutic. Molecular Biology Reports. 2025;52(1):347.
  23. Chen J., Liu J., Nie W., Hou X., Zhang X., Liu C., et al. Structural and anti-colorectal cancer properties of shikonin. Journal of Cancer Research and Therapeutics. 2024;20(7):1957–1963.
  24. Liu Y., Fang C., Luo J., Gong C., Wang L., Zhu S. Traditional Chinese medicine for cancer treatment. American Journal of Chinese Medicine. 2024;52(3):583–604.
  25. Xu J., Koizumi K., Liu M., Mizuno Y., Suzaki M., Iitsuka H., et al. Shikonin induces antitumor effects via p38-dependent apoptosis. Oncology Reports. 2019;41(3):2020–2026.
  26. Elimam H., Alhamshry N.A.A., Hatawsh A., Elfar N., Moussa R., Radwan A.F., et al. Natural products and lncRNA signatures in gallbladder cancer. Naunyn-Schmiedeberg’s Archives of Pharmacology. 2024;397(12):9549–9571.
  27. Zhang C-H., Wang J., Zhang L-X., Lu Y-H., Ji T-H., Xu L., et al. Shikonin reduces tamoxifen resistance through lncRNA uc.57. Oncotarget. 2017;8(51):88658–88670.
  28. Wang Y., Bu N., Luan X., Song Q., Ma B-F., Hao W., et al. Long non-coding RNAs in breast cancer resistance. Frontiers in Oncology. 2024;14:1337579.
  29. Lin K-H., Huang M-Y., Cheng W-C., Wang S-C., Fang S-H., Tu H-P., et al. RNA-seq analysis of breast cancer cells under shikonin treatment. Scientific Reports. 2018;8(1):2672.
  30. Fan J., Cao S., Chen M., Yao Q., Zhang X., Du S., et al. AC079305/DUSP1 axis in ischemic stroke. Oxidative Medicine and Cellular Longevity. 2022;2022:8432352.
  31. Hu Y., Zai H., Jiang W., Ou Z., Yao Y., Zhu Q. Exosomal lncRNA NEAT1 induces tumor-supporting myofibroblasts. Journal of Oncology. 2022;2022:7630698.
  32. Wei F., Yan Z., Zhang X., Wang Y., Wang M., Zhu Y., et al. LncRNA-NEAT1 in pancreatic cancer. Biotechnology and Genetic Engineering Reviews. 2024;40(2):1094–1112.
  33. Mao M., Zheng X., Sheng Y., Chai J., Ding H. Evodiamine inhibits ovarian cancer via NEAT1/miR-152-3p/CDK19. Chemical Biology and Drug Design. 2023;102(1):101–114.
  34. Bai J., Huang G. Role of lncRNA NEAT1 in prostate cancer prognosis. Medicine. 2020;99(22):e20204.
  35. Zang F., Rao Y., Zhu X., Wu Z., Jiang H. Shikonin suppresses NEAT1 and Akt signaling. Molecular Medicine. 2020;26(1):1–7.
  36. Meng J., Li P., Zhang Q., Yang Z., Fu S. A four-lncRNA signature predicting breast cancer survival. Journal of Experimental and Clinical Cancer Research. 2014;33(1):1–10.
  37. Zanoni M., Bravaccini S., Fabbri F., Arienti C. Aldehyde dehydrogenase isoforms in therapy resistance. Frontiers in Medicine. 2022;9:795762.
  38. McLean M.E., MacLean M.R., Cahill H.F., Arun R.P., Walker O.L., Wasson M-C.D., et al. ALDH1A3 in cancer. Cancers. 2023;15(2):492.
  39. Marcato P., Dean C.A., Pan D., Araslanova R., Gillis M., Joshi M., et al. ALDH1A3 in breast cancer metastasis. Stem Cells. 2011;29(1):32–45.
  40. Yao Y., Li N. MIR600HG enhances chemosensitivity in colorectal cancer. Bioscience Reports. 2020;40(4):BSR20200390.
  41. Chateauvieux S., Gaigneaux A., Gérard D., Orsini M., Morceau F., Orlikova-Boyer B., et al. Inflammation regulates lncRNA-PTTG1-1 in leukemia. Haematologica. 2020;105(6):e280.
  42. Yi Y., Fang Y., Wu K., Liu Y., Zhang W. Gene and pathway analysis of cervical cancer progression. Oncology Letters. 2020;19(4):3316–3332.
  43. Wang D., Chen Z., Yeung A.W.K., Atanasov A.G. Endothelial cell model differences revealed by transcriptomics. Current Research in Biotechnology. 2021;3:135–145.
  44. Wang J., Koganti P.P., Yao J., Wei S., Cleveland B. lncRNAs in rainbow trout skeletal muscle under estradiol exposure. Scientific Reports. 2017;7(1):11780.
  45. Looi C-K., Hii L-W., Ngai S.C., Leong C-O., Mai C-W. Role of Rap1 in cancer. Biomedicines. 2020;8(9):334.
  46. Zhang Y-L., Wang R-C., Cheng K., Ring B.Z., Su L. Rap1 signaling in tumor migration. Cancer Biology and Medicine. 2017;14(1):90–99.
  47. Colin D.J., Hain K.O., Allan L.A., Clarke P.R. Cellular responses to prolonged mitotic delay. Open Biology. 2015;5(3):140156.
  48. Dini S., Ghorbani A., Eskandarzadeh N., Alibeiki M. Long non-coding RNAs associated with breast cancer cell apoptosis following resveratrol treatment: an in silico analysis. Veterinary and Comparative Biomedical Research. 2025;2(2):1–10.
آمار
تعداد مشاهده مقاله: 228
تعداد دریافت فایل اصل مقاله: 131


counter
سامانه مدیریت نشریات علمی. طراحی و پیاده سازی از سیناوب