Team:Ain Shams-Egypt/Description
Project Description Abstract: Treatment options for HCC are limited and often inefficient. Anti-cancer therapy faces major challenges, particularly in terms of specificity of treatment. The ideal therapy would eradicate tumor cells selectively with minimum side effects on normal tissue.
So as a team that believes in synthetic biology we searched how could we help our community regarding this problem & we found that it’s been shown that circular RNA (circ.RNA) is associated with human cancers, & some studies have been reported in HCC. Circular RNA will be delivered as it is a new area of research with around 130 circular RNA sequence detected in HCC only less than 10% of these has been investigated and characterized through previous studies.
Circular RNA is a type of RNA which, that forms a covalently closed continuous loop. This feature confers numerous properties to circular RNAs, many of which have only recently been identified. Circular RNAs have recently shown potential as gene regulators. Like many other alternative noncoding isoforms, the biological function of most circular RNAs are unclear, circular RNAs do not have 5' or 3' ends so they are resistant to exonuclease-mediated degradation and more stable than most linear RNAs in cells.
Hepatocellular carcinoma (HCC) is one of the most common malignancies and one of the leading causes of cancer-related death globally .Circular RNAs (circRNAs) are a large class of RNAs that, unlike linear RNAs, form covalently closed continuous loops and have recently shown huge capabilities as gene regulators in mammals [1] .
Interestingly, they are found to be enormously abundant, evolutionally conserved and relatively stable in cytoplasm. These features confer numerous potential functions to circRNAs, such as acting as microRNA (miRNA) sponges, binding to RNA-associated proteins to form RNA-protein complexes and then regulating gene transcription. Importantly, circRNAs associate with cancer-related miRNAs and the circRNA-miRNA axes are involved in cancer-related pathways. Some synthetic circRNAs have shown remarkable anti-cancer effects [2] . The current methods to detect and characterize circRNAs are still limited and challenge-able [3 ]. The emerging roles of the highly complex network of circRNAs, which communicate via miRNA and the overwhelming number of identified circRNA structures leads to exciting new avenues of research to uncover the full biologic functions of these n cRNAs in cellular regulation and human disease. The clinical trial treating some human diseases with synthetic miRNA inhibitors is already in phase 2a [4 ]. Like these small RNA-based drugs (e.g. miRNAs), such circRNA molecules face multiple delivery challenges such as lack of targeted delivery in cancer targeted therapy [5 ].
Recently, researchers used circular sponge activity help in countering harmful miRNA activity.The circularized miRNA sponges displayed superior anti-cancer activities compared to the linear sponges in malignant melanoma cell lines [6] . As an alternative to the use of the vectors expressing linear sponges, the use of the expression vector for RNA circles opens new way to deliver miRNA sponges with persistent effects. The availability of circularizing the miRNA sponge in cells is a candidate for a new methodology for RNA-based cancer therapy [7] . Since certain circRNA has many binding sites for a specific miRNA, it is more effective than typical miRNA inhibitors . With the new discovery of miRNA management by naturally occurring circRNAs, RNA circles may prove to be well-suited decoy-type miRNA inhibitors serving as new generation of miRNA inhibitors[8]. Such synthetic circRNA inhibitors might be future targets for therapies and soon appear as new therapeutic strategies in cancers. For this project, we will use a variety of computational algorithms for the prediction of a set of a cirRNA and a selected competing endogenous RNA involved in HCC development .Finally, we will establish functional hypothesis for the cirRNA network in HCC using public microarray public database to identify molecular signatures associated with HCC . We will adopt a novel strategy for miRNA suppression by using circRNAs. These findings may provide the rationale for designing novel therapeutic approaches using artificial synthetic circuit modulating dysregulated circular RNA network. GOAL: To evaluate the therapeutic efficacy of Circular RNA-miRNA based synthetic circuit in hepatocellular carcinoma cell line.
Objectives: The core of the project is to retrieve cirRNA and a selected competing endogenous RNA related to HCC development and progression.Secondly, we will investigate whether synthetic circRNAs modulator exerts an ameliorative effect in HCC using HCC cell line and addressing the mechanism involved in modulating cirRNA expression. It is anticipated that we will likely identify the ciRNA loop associated with HCC, thus posing the basis for the possible harnessing of these cirRNAs as therapeutic targets, as well as possible diagnostic-prognostic tools. Moreover, we will adopt promising strategies for better management of HCC through modulation of dysregulated cirRNA specific for HCC .Moreover, we may end up with alternative strategies for better management of HCC through the gate of synthetic biology.
Research Approach: 1- To analyze cirRNA and disease databases to select relevant cirRNA for HCC through cirBase and Circ2Traits databases.
2- To analyze cirRNA-miRNA interaction databases to retrieve competing endogenous RNA specific for HCC through Circular RNA interactome database and Starbase database.
3- In silico design of Circular RNA-miRNA based synthetic circuit to modulate the deregulated expression in HCC based on the following points
System: Should be able to release specific CircRNA in response to the deregulation(increase) in the specific miRNA.
Circuit: Should have our specific miRNA as an input and our CircRNA as an output, and a regulatory component.
Devices: We need to put a sensing device(sensory arm) and an effector device or effector arm in addition to a reporter device to reflect the circuit status.
Parts: Physical components and DNA.
4- To investigate the effects and mechanism of the chosen cirRNA expression on the proliferation of HCC cell line by transfecting the artificial synthetic circuit into cultured cells to manipulate cirRNA
5- To characterize the efficacy of artificial synthetic circuit on modulating cirRNA and HCC proliferation in HCC cell line and animal model
References :
1 Salzman, J., Chen, R. E., Olsen, M. N., Wang, P. L. & Brown, P. O. Cell-type specific features of circular RNA expression. PLoS Genet 9, e1003777 (2013).
2 Hansen,T. B.etal.NaturalRNAcirclesfunctionasefficientmicroRNAsponges. Nature 495, 384–388 (2013).
3 Guo JU, Agarwal V, Guo H and BartelDP.Expanded identification and characterization of mammalian circular RNAs. Genome Biol 2014; 15: 409.
4 Janssen HL, Reesink HW, Lawitz EJ, Zeuzem S, Rodriguez-Torres M, Patel K, van der Meer AJ, Patick AK, Chen A, Zhou Y, Persson R, King BD, Kauppinen S, Levin AA and Hodges MR. Treatment of HCV infection by targeting microRNA. N Engl J Med 2013; 368: 1685-1694.
5 Gong Z, Yang J, Li J, Yang L, Le Y, Wang S and Lin HK. Novel insights into the role of microRNA in lung cancer resistance to treatment and targeted therapy.Curr Cancer Drug Targets 2014; 14: 241-258.
6 Tay FC, Lim JK, Zhu H, Hin LC and Wang S. Using artificial microRNA sponges to achieve microRNA loss-of-function in cancer cells. Adv Drug Deliv Rev 2015; 81: 117-127
7 Bak RO, Hollensen AK and MikkelsenJG.Managing microRNAs with vector-encoded decoytypeinhibitors.MolTher 2013; 21: 14781485.
8 Haraguchi T, Ozaki Y and Iba H. Vectors expressing efficient RNA decoys achieve the long-term suppression of specific microRNA activity in mammalian cells. Nucleic Acids Res 2009; 37: e43.
