Employing in Silico Investigations to Determine the Cross-kingdom Approach for MiRNAs and Their Human Targets

Overview

Journal Beni Suef Univ J Basic Appl Sci

Publisher Springer Nature

Date 2023 Jan 16

PMID 36644780

Authors

Atiyabanu N Saiyed

Abhay R Vasavada

S R Kaid Johar

Affiliations

Soon will be listed here.

Abstract

Background: Plant elements and extracts have been used for centuries to treat a wide range of diseases, from cancer to modern lifestyle ailments like viral infections. These plant-based miRNAs have the capacity to control physiological and pathological conditions in both humans and animals, and they might be helpful in the detection and treatment of a variety of diseases. The present study investigates the miRNA of the well-known spice and its prospective targets using a variety of bioinformatics techniques.

Results: Using the integrative database of animal, plant, and viral microRNAs known as miRNEST 2.0, nine miRNAs were predicted. psRNA target service foretells the presence of 23 human target genes linked to a variety of disorders. By interacting with a variety of cellular and metabolic processes, miRNAs 167, 1525, and 756 have been found to be critical regulators of tumour microenvironment. SARS-cov2 and influenza A virus regulation have been connected to ZFP36L1 from miRNA 1525 and ETV5 from miRNA 756, respectively.

Conclusions: The current cross-kingdom study offers fresh knowledge about how to increase the effectiveness of plant-based therapies for disease prevention and serves as a platform for and research development.

Graphical Abstract:

References

Hedl M, Abraham C . A TNFSF15 disease-risk polymorphism increases pattern-recognition receptor-induced signaling through caspase-8-induced IL-1. Proc Natl Acad Sci U S A. 2014; 111(37):13451-6. PMC: 4169936. DOI: 10.1073/pnas.1404178111. View

Patel M, Patel S, Mangukia N, Patel S, Mankad A, Pandya H . Ocimum basilicum miRNOME revisited: A cross kingdom approach. Genomics. 2018; 111(4):772-785. DOI: 10.1016/j.ygeno.2018.04.016. View

Kumar D, Kumar S, Ayachit G, Bhairappanavar S, Ansari A, Sharma P . Cross-Kingdom Regulation of Putative miRNAs Derived from Happy Tree in Cancer Pathway: A Systems Biology Approach. Int J Mol Sci. 2017; 18(6). PMC: 5486014. DOI: 10.3390/ijms18061191. View

Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J . STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 2014; 43(Database issue):D447-52. PMC: 4383874. DOI: 10.1093/nar/gku1003. View

Kang H . MicroRNA-Mediated Health-Promoting Effects of Phytochemicals. Int J Mol Sci. 2019; 20(10). PMC: 6566171. DOI: 10.3390/ijms20102535. View

Gadhavi H, Patel M, Mangukia N, Shah K, Bhadresha K, Patel S . Transcriptome-wide miRNA identification of : a cross-kingdom approach. Plant Signal Behav. 2019; 15(1):1699265. PMC: 7012157. DOI: 10.1080/15592324.2019.1699265. View

Chen X, Liu L, Chu Q, Sun S, Wu Y, Tong Z . Large-scale identification of extracellular plant miRNAs in mammals implicates their dietary intake. PLoS One. 2021; 16(9):e0257878. PMC: 8480717. DOI: 10.1371/journal.pone.0257878. View

Du R, Huang C, Chen H, Liu K, Xiang P, Yao N . SDCBP/MDA-9/syntenin phosphorylation by AURKA promotes esophageal squamous cell carcinoma progression through the EGFR-PI3K-Akt signaling pathway. Oncogene. 2020; 39(31):5405-5419. DOI: 10.1038/s41388-020-1369-2. View

Zhou G, Soufan O, Ewald J, Hancock R, Basu N, Xia J . NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis. Nucleic Acids Res. 2019; 47(W1):W234-W241. PMC: 6602507. DOI: 10.1093/nar/gkz240. View

10.

Bhuiyan F, Howlader S, Raihan T, Hasan M . Plants Metabolites: Possibility of Natural Therapeutics Against the COVID-19 Pandemic. Front Med (Lausanne). 2020; 7:444. PMC: 7427128. DOI: 10.3389/fmed.2020.00444. View

11.

Saiyed A, Vasavada A, Johar S . Recent trends in miRNA therapeutics and the application of plant miRNA for prevention and treatment of human diseases. Futur J Pharm Sci. 2022; 8(1):24. PMC: 8972743. DOI: 10.1186/s43094-022-00413-9. View

12.

Kozomara A, Birgaoanu M, Griffiths-Jones S . miRBase: from microRNA sequences to function. Nucleic Acids Res. 2018; 47(D1):D155-D162. PMC: 6323917. DOI: 10.1093/nar/gky1141. View

13.

Helfricht A, Thijssen P, Rother M, Shah R, Du L, Takada S . Loss of ZBTB24 impairs nonhomologous end-joining and class-switch recombination in patients with ICF syndrome. J Exp Med. 2020; 217(11). PMC: 7526497. DOI: 10.1084/jem.20191688. View

14.

Chin C, Chen S, Wu H, Ho C, Ko M, Lin C . cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Syst Biol. 2014; 8 Suppl 4:S11. PMC: 4290687. DOI: 10.1186/1752-0509-8-S4-S11. View

15.

Lorenz R, Bernhart S, Honer Zu Siederdissen C, Tafer H, Flamm C, Stadler P . ViennaRNA Package 2.0. Algorithms Mol Biol. 2011; 6:26. PMC: 3319429. DOI: 10.1186/1748-7188-6-26. View

16.

Zhang L, Hou D, Chen X, Li D, Zhu L, Zhang Y . Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA. Cell Res. 2011; 22(1):107-26. PMC: 3351925. DOI: 10.1038/cr.2011.158. View

17.

Titze de Almeida S, Horst C, Soto-Sanchez C, Fernandez E, Titze de Almeida R . Delivery of miRNA-Targeted Oligonucleotides in the Rat Striatum by Magnetofection with Neuromag. Molecules. 2018; 23(7). PMC: 6099620. DOI: 10.3390/molecules23071825. View

18.

Suzuki I, Gacquer D, Van Heurck R, Kumar D, Wojno M, Bilheu A . Human-Specific NOTCH2NL Genes Expand Cortical Neurogenesis through Delta/Notch Regulation. Cell. 2018; 173(6):1370-1384.e16. PMC: 6092419. DOI: 10.1016/j.cell.2018.03.067. View

19.

OBrien J, Hayder H, Zayed Y, Peng C . Overview of MicroRNA Biogenesis, Mechanisms of Actions, and Circulation. Front Endocrinol (Lausanne). 2018; 9:402. PMC: 6085463. DOI: 10.3389/fendo.2018.00402. View

20.

Zuker M . Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003; 31(13):3406-15. PMC: 169194. DOI: 10.1093/nar/gkg595. View