Onion Extract on Cell Gene Expression Profile: a System Biology Approach

Document Type : Original paper

Authors

1 Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.

2 Laser Application in Medical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

3 Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

4 Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

5 Traditional Medicine and Materia Medica Research Center and Department of Traditional Medicine, School of Traditional Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

Abstract

Background and objectives: Widespread consuming of onion as a nutrient in the world implies more investigations about useful and harmful aspects of this common supplementary food. Assessment of molecular mechanism of yellow onion extract on cell line Caco-2 was the aim of this study. Methods: Data was extracted from gene expression omnibus (GEO) database. The gene expression profiles of Caco-2 cells in the presence of yellow onion extract versus control cells were analyzed via GOE2R software. The significant differentially expressed genes (DEGs) were assessed via network analysis and the central nodes were enriched via gene ontology. Results: Thirteen central nodes including JUN, ATF3, DUSP1 VEGF, CDKN1A, SNAI1, HSPB1, MCL1, SQSTM1, SREBF1, MAP1LC3B, EZR, and DUSP5 were identified. The related biological terms in five groups were introduced. JUN as a crucial DEG was highlighted. Conclusion: Based on findings, yellow onion extract effects on the wide range of cellular function such as apoptosis, cell proliferation and more other vital functions. The significant role of c-Jun proto-oncogene (among JUN, ATF3, and DUSP1 as hub-bottlenecks) and “c-Jun-ATF3 complex” biological term group as the affected individuals by yellow onion extract were pointed in this study.

Keywords

Main Subjects


  • Cheng A, Chen X, Jin Q, Wang W, Shi J, Liu Y. Comparison of phenolic content and antioxidant capacity of red and yellow onions. Czech J Food Sci. 2013; 31(5): 501–508.
  • Shon MY, Choi SD, Kahng GG, Nam SH, Sung NJ. Antimutagenic, antioxidant and free radical scavenging activity of ethyl acetate extracts from white, yellow and red onions. Food Chem Toxicol. 2004; 42(4): 659–666.
  • Ahmadi S, Rajabi Z, Vasfi Marandi M. Evaluation of the antiviral effects of aqueous extracts of red and yellow onions (Allium cepa) against avian influenza virus subtype H9N2. Iran J Vet Sci Technol. 2018; 10(2): 23–27.
  • Montaner J, Ramiro L, Simats A, Tiedt S, Makris K, Jickling GC, Debette S, Sanchez JC, Bustamante Multilevel omics for the discovery of biomarkers and therapeutic targets for stroke. Nat Rev Neurol. 2020; 16(5): 247–264.
  • Zaynab M, Fatima M, Abbas S, Sharif Y, Jamil K, Ashraf A, Muhammad Aslam M, Shabbir A, Batool W. Proteomics approach reveals importance of herbal plants in curing diseases. Mol Microbiol. 2018; 1(1): 23–28.
  • Chakraborty P. Herbal genomics as tools for dissecting new metabolic pathways of unexplored medicinal plants and drug discovery. Biochim Open. 2018; 6: 9–16.
  • Liu L, Wang H. The recent applications and developments of bioinformatics and omics technologies in traditional chinese medicine. Curr Bioinform. 2019; 14(3): 200–210.
  • Scott Boyer M, Lacroix S, Scotti M, Morine M, Kaput J, Priami C. Scientific reports 2016: a network analysis of cofactor-protein interactions for analyzing associations between human nutrition and diseases. J Aust Trad-Med Soc. 2016; 22(1): 45–46.
  • Jafarpour Sadegh F, Montazeri V, Adili A, Esfehani A, Rashidi MR, Pirouzpanah S. Consumption of fresh yellow onion ameliorates hyperglycemia and insulin resistance in breast cancer patients during doxorubicin-based chemotherapy: a randomized controlled clinical trial. Integr Cancer Ther. 2017; 16(3): 276–289.
  • Sanz Pamplona R, Berenguer A, Sole X, Cordero D, Crous Bou M, Serra Musach J, Guinó E, Ángel Pujana M, Moreno Tools for protein-protein interaction network analysis in cancer research. Clin Transl Oncol. 2012; 14(1): 3–14.
  • Dietz KJ, Jacquot JP, Harris G. Hubs and bottlenecks in plant molecular signalling networks. New Phytol. 2010; 188(4): 919–938.
  • Nuoroozi G, Mirmotalebisohi SA, Sameni M, Arianmehr Y, Zali H. Deregulation of microRNAs in oral squamous cell carcinoma, a bioinformatics analysis. Gene Rep. 2021; Article ID 101241.
  • Rezaei Tavirani M, Rezaei Tavirani S, Mansouri V, Rostami Nejad M, Rezaei Tavirani M. Protein-protein interaction network analysis for a biomarker panel related to human esophageal adenocarcinoma. Asian Pac J Cancer Prev. 2017; 18(12): 3357–3363.
  • Arjmand B, Zamanian Azodi M, Rezaei Tavirani M, Esmaeili S, Vafaee R. Contradictory effects of 6-shogaol on the human cervical cancer cell line HeLa through network analysis. Res J Pharmacogn. 2022; 9(1): 29–37.
  • Arjmand B, Zamanian Azodi M, Rezaei Tavirani M, Khodadoost M, Rostami Nejad M, Ahmadi N. Tumorigenesis inhibition of carnosol from rosemary: an insight to molecular targeting. Res J Pharmacogn. 2022; 9(1): 103–110.
  • Zamanian Azodi M, Rezaei Tavirani M, Esmaeili S, Arjmand B, Jahani Sherafat S. Evaluation of anticancer effect of ghost pepper: a bioinformatics assessment. Res J Pharmacogn. 2021; 8(3): 77–82.
  • de Wit NJ, Hulst M, Govers C, van der Meulen J, van Hoef A, Stoopen G, Hamers A, Hoekman A, de Vos R, Bovee TFH, Smits M, Mes JJ, Hendriksen PJM. Effects of digested onion extracts on intestinal gene expression: an interspecies comparison using different intestine models. PLoS One. 2016; 11(9): 1–18.
  • Zali H, Zamanian Azodi M, Rezaei Tavirani M, Akbar Zadeh Baghban Protein drug targets of Lavandula angustifolia on treatment of rat Alzheimer's disease. Iran J Pharm Res. 2015; 14(1): 291–302.
  • Wolf YI, Karev G, Koonin EV. Scale‐free networks in biology: new insights into the fundamentals of evolution? Bioessays. 2002; 24(2): 105–109.
  • Abbaszadeh HA, Peyvandi AA, Sadeghi Y, Safaei A, Zamanian Azodi M, Khoramgah MS, Rezaei Tavirani M. Er: YAG laser and cyclosporin a effect on cell cycle regulation of human gingival fibroblast cells. J Lasers Med Sci. 2017; 8(3): 143–149.
  • Karbalaei R, Allahyari M, Rezaei Tavirani M, Asadzadeh Aghdaei H, Zali MR. Protein-protein interaction analysis of Alzheimers disease and NAFLD based on systems biology methods unhide common ancestor pathways. Gastroenterol Hepatol Bed Bench. 2018; 11(1): 27–33.
  • De Groot R, Sassone Corsi P. Activation of Jun/AP-1 by protein kinase A. Oncogene. 1992; 7(11): 2281–2286.
  • Vogt PK. Fortuitous convergences: the beginnings of JUN. Nat Rev Cancer. 2002; 2(6): 465–469.
  • Meng Q, Xia Y. c-Jun, at the crossroad of the signaling network. Protein Cell. 2011; 2(11): 889–898.
  • Li J, Pan C, Boese AC, Kang J, Umano AD, Magliocca KR, Yang W, Zhang Y, Lonial S, Jin L, Kang DGKA provides platinum resistance in ovarian cancer through activation of c-JUN–WEE1 signaling. Clin Cancer Res. 2020; 26(14): 3843–3855.
  • Kumar M, Barbhai MD, Hasan M, Punia S, Dhumal S, Rais N, Chandran D, Pandiselvam R, Kothakota A, Tomar M, Satankar V, Senapathy M, Anitha T, Dey A, Sayed AAS, Gadallah FM, Amarowicz R, Mekhemar Onion (Allium cepa L.) peels: a review on bioactive compounds and biomedical activities. Biomed Pharmacother. 2022; 146: 1–15.
  • Sykes SM, Di Marcantonio D, Martinez E, Huhn J, Gupta A, Mistry R. JUN and ATF3 regulate the transcriptional output of the unfolded protein response to support acute myeloid leukemia. Blood. 2018; 132(S1): 1–3.
  • Zhou M, Ou Y, Wu G, Li K, Peng J, Wang X, Che M, Gong H, Niu P, Liu Y, Feng Z, Qi Transcriptomic analysis reveals that Atf3/c-Jun/Lgals3 axis is associated with central diabetes insipidus after hypothalamic injury. Neuroendocrinology. 2021; 112(9): 874–893.