Integrative transcriptome analysis of triple negative breast cancer profiles for identification of druggable targets

References

• Abbasi, B. A., Iqbal, J., Ahmad, R., Bibi, S., Mahmood, T., Kanwal, S., Bashir, S., Gul, F., & Hameed, S. (2019). Potential phytochemicals in the prevention and treatment of esophagus cancer: A green therapeutic approach. Pharmacological Reports, 71(4), 644–652. https://doi.org/10.1016/j.pharep.2019.03.001
   PubMed Web of Science ®Google Scholar
• Berry, J. T. L., Muñoz, L. E., Stewart, R. M. R., Selvaraj, P., & Mainou, B. A. (2020). Doxorubicin conjugation to reovirus improves oncolytic efficacy in triple-negative breast cancer. Molecular Therapy Oncolytics, 18, 556–572. https://doi.org/10.1016/j.omto.2020.08.008
   PubMed Web of Science ®Google Scholar
• Fei, H., Chen, S., & Xu, C. (2020). RNA-sequencing and microarray data mining revealing: the aberrantly expressed mRNAs were related with a poor outcome in the triple negative breast cancer patients. Annals of Translational Medicine, 8(6), 363–363. https://doi.org/10.21037/atm.2020.02.51
   PubMed Web of Science ®Google Scholar
• Israel, B. E. B., Tilghman, S. L., Parker-Lemieux, K., & Payton-Stewart, F. (2018). Phytochemicals: Current strategies for treating breast cancer. Oncology Letters, 15(5), 7471–7478. https://doi.org/10.3892/ol.2018.8304
   PubMed Web of Science ®Google Scholar
• Kulkarni, A., Kelkar, D. A., Parikh, N., Shashidhara, L. S., Koppiker, C. B., & Kulkarni, M. (2020). Meta-analysis of prevalence of triple-negative breast cancer and its clinical features at incidence in indian patients with breast cancer. JCO Global Oncology, 6, 1052–1062. https://doi.org/10.1200/GO.20.00054
   PubMedGoogle Scholar
• Lamb, J., Crawford, E. D., Peck, D., Modell, J. W., Blat, I. C., Wrobel, M. J., Lerner, J., Brunet, J.-P., Subramanian, A., Ross, K. N., Reich, M., Hieronymus, H., Wei, G., Armstrong, S. A., Haggarty, S. J., Clemons, P. A., Wei, R., Carr, S. A., Lander, E. S., & Golub, T. R. (2006). The connectivity map: Using gene-expression signatures to connect small molecules, genes, and disease. Science (New York, N.Y.), 313(5795), 1929–1935. https://doi.org/10.1126/science.1132939
   PubMed Web of Science ®Google Scholar
• Livak, K. J., & Schmittgen, T. D. (2001). Analysis of relative gene expression data using real-time quantitative PCR and the 2 − ΔΔCT method. Methods (San Diego, Calif.), 25(4), 402–408. https://doi.org/10.1006/meth.2001.1262
   PubMed Web of Science ®Google Scholar
• Majolo, F., Delwing, L., Marmitt, D. J., Bustamante-Filho, I. C., & Goettert, M. I. (2019). Medicinal plants and bioactive natural compounds for cancer treatment: Important advances for drug discovery. Phytochemistry Letters, 31, 196–207. https://doi.org/10.1016/j.phytol.2019.04.003
   Web of Science ®Google Scholar
• Midorikawa, Y., Yamamoto, S., Tatsuno, K., Renard-Guillet, C., Tsuji, S., Hayashi, A., Ueda, H., Fukuda, S., Fujita, T., Katoh, H., Ishikawa, S., Covington, K. R., Creighton, C. J., Sugitani, M., Wheeler, D. A., Shibata, T., Nagae, G., Takayama, T., & Aburatani, H. (2020). Accumulation of molecular aberrations distinctive to hepatocellular carcinoma progression. Cancer Research, 80(18), 3810–3819. https://doi.org/10.1158/0008-5472.CAN-20-0225
   PubMed Web of Science ®Google Scholar
• Muthuswami, M., Ramesh, V., Banerjee, S., Thangaraj, S. V., Periasamy, J., Rao, D. B., Barnabas, G. D., Raghavan, S., & Ganesan, K. (2013). Breast tumors with elevated expression of 1q candidate genes confer poor clinical outcome and sensitivity to Ras/PI3K inhibition. PLoS One, 8(10), e77553. https://doi.org/10.1371/journal.pone.0077553
   PubMed Web of Science ®Google Scholar
• Oliveros, J. C. (2007–2015). Venny. An interactive tool for comparing lists with Venn’s diagrams. http://bioinfogp.cnb.csic.es/tools/venny/index.html
   Google Scholar
• Pandit, K., Kaur, S., Kumar, A., Bhardwaj, R., & Kaur, S. (2020). Trans-anethole abrogates cell proliferation and induces apoptosis through the mitochondrial-mediated pathway in human osteosarcoma cells. Nutrition and Cancer, 9, 1–19.
   Google Scholar
• Patel, N., Weekes, D., Drosopoulos, K., Gazinska, P., Noel, E., Rashid, M., Mirza, H., Quist, J., Brasó-Maristany, F., Mathew, S., Ferro, R., Pereira, A. M., Prince, C., Noor, F., Francesch-Domenech, E., Marlow, R., de Rinaldis, E., Grigoriadis, A., Linardopoulos, S., Marra, P., & Tutt, A. N. J. (2018). Integrated genomics and functional validation identifies malignant cell specific dependencies in triple negative breast cancer. Nature Communications, 9(1), 16. https://doi.org/10.1038/s41467-018-03283-z
   PubMedGoogle Scholar
• Sharma, S., Tanwar, A., & Gupta, D. K. (2016). Curcumin: An adjuvant therapeutic remedy for liver cancer. Hepatoma Research, 2(3), 62–70. https://doi.org/10.20517/2394-5079.2015.59
   Google Scholar
• Sipos, O., Tovey, H., Quist, J., Haider, S., Nowinski, S., Gazinska, P., Kernaghan, S., Toms, C., Maguire, S., Orr, N., Linn, S. C., Owen, J., Gillett, C., Pinder, S. E., Bliss, J. M., Tutt, A., Cheang, M. C. U., & Grigoriadis, A. (2021). Assessment of structural chromosomal instability phenotypes as biomarkers of carboplatin response in triple negative breast cancer: The TNT trial. Annals of Oncology: Official Journal of the European Society for Medical Oncology, 32(1), 58–65. https://doi.org/10.1016/j.annonc.2020.10.475
   PubMed Web of Science ®Google Scholar
• Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., & Mesirov, J. P. (2005). Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America, 102(43), 15545–15550. https://doi.org/10.1073/pnas.0506580102
   PubMed Web of Science ®Google Scholar
• Tang, D., Zhao, X., Zhang, L. I., Wang, Z., & Wang, C. (2019). Identification of hub genes to regulate breast cancer metastasis to brain by bioinformatics analyses. Journal of Cellular Biochemistry, 120(6), 9522–9531. https://doi.org/10.1002/jcb.28228
   PubMed Web of Science ®Google Scholar
• Yan, P., Tang, L., Liu, L., & Tu, G. (2020). Identification of candidate RNA signatures in triple-negative breast cancer by the construction of a competing endogenous RNA network with integrative analyses of gene expression omnibus and the cancer genome Atlas data. Oncology Letters, 19(3), 1915–1927. https://doi.org/10.3892/ol.2020.11292
   PubMed Web of Science ®Google Scholar
• Yang, X., Kui, L., Tang, M., Li, D., Wei, K., Chen, W., Miao, J., & Dong, Y. (2020). High-throughput transcriptome profiling in drug and biomarker discovery. Frontiers in Genetics, 11, 19. https://doi.org/10.3389/fgene.2020.00019
   PubMed Web of Science ®Google Scholar