In recent years, mi-RNAs regulating protein translation rates and mRNA degradation rates have been the subject of intensive studies. Reports on new miRNA types and their role in posttranscriptional regulation are being published continuously. Additionally, mathematical models are being developed and used in investigation of robustness of the regulatory mechanisms based on miRNA as well as dynamics of the regulatory processes. The latter issue may be of great importance if miRNAs are used as a way to exert control over intracellular processes.

The main goal of this work is not to propose a new model of miRNA involvement in regulation of any particular signaling pathway. Instead, it is concerned with the impact of experimental techniques on the observed results. These techniques involve  micro-injections of siRNA, miRNA transfection and transfection of targets for a given miRNA. In each case, the observed results are usually used to draw conclusions about the role a particular miRNA may play in a given cell type or the dynamics of changes in cellular responses to external stimuli that are the direct outcome of miRNA actions. However, transfections or microinjections might themselves contribute significantly to these changes, and it might happen that the observed results are the artifacts of experimental procedures.

Therefore, we use numerical simulations to check under what assumptions the experimental procedures do not affect predominantly cellular responses. We use both mathematical models from recent publications (among others Hausser et al., 2013, Xue et al., 2013, Yan et al., 2014) and a simple generic model we have built for that purpose. We show that in some cases, the conclusions drawn from experiments are valid, while in other cases what is observed is just the response of the cell to a large extent of the molecules that entered the cell.

Additionally, we analyze the effect of heterogeneity of cellular responses on the observations performed at the cell population level (e.g. in which the amount of mRNA is measured using PCR techniques, protein or protein complexes levels are checked with Western blot techniques etc.  - all these methods result in averaging over population). In the experiments under consideration, the natural heterogeneity of cellular behavior is amplified by the stochastic nature of the transfection processes.

References

Hausser et.al., Timescales and bottlenecks in miRNA-dependent gene regulation. Mol Syst Biol. 2013

Xue et al., A modeled dynamic regulatory network of NF-κB and IL-6 mediated by miRNA. Biosystems. 2013

Yan et al. Dynamic analysis of the combinatorial regulation involving transcription factors and microRNAs in cell fate decisions. Biochim Biophys Acta. 2014