Dr. Nuno Rocha Nene

My PhD project aimed at understanding how cell fate decision emerges from the overall intracellular network connectivity and dynamics. To achieve this goal both small paradigmatic signalling-gene regulatory networks and their generalization to high-dimensional space were tested. Particularly, we drew special attention to the importance of the effects of time varying parameters in the decision genetic switch with external stimulation.

The most striking feature of our findings is the clear and crucial impact of the rate with which the time- dependent parameters are changed. In the presence of small asymmetries and fluctuations, slow passage through the critical region increases substantially specific attractor selection by external transient perturbations. This has strong implications for the cell fate decision problem since cell phenotype in stem cell differentiation, cell cycle progression, or apoptosis studies, has been successfully identified as attractors of a whole network expression process induced by signalling events. Moreover, asymmetry and noise naturally exist in any integrative intra-cellular decision network.

To further clarify the importance of the rate of parameter sweeping, we also studied models from non-equilibrium systems theory. These are traditional in the study of phase transitions in statistical physics and stood as a fundamental tool to extrapolate key results to intracellular network dynamics. Specifically, we analysed the effects of a time- dependent asymmetry in the canonical supercritical pitchfork bifurcation model, both by numerical simulations and analytical solutions. We complemented the discussion of cell fate decision with a study of the effects of non-specific targets of drugs on the Epidermal Growth Factor Receptor pathway. Pathway output has long been correlated with qualitative cell phenotype. Cancer network multi- targeting therapies were assessed in the context of whole network attractor phenotypes and the importance of parameter sweeping speed.



Publications:

N.R. Nene, A. Zaikin. Gene expression pattern selection induced by high-order targeting
strategies. (in preparation)
N.R. Nene, A. Zaikin. Parametrically-driven double-well potential response to external
transient perturbations. (in preparation)
N.R. Nene, A. Zaikin. Speed-dependent gene network decision in paradigmatic
bifurcation cellular dynamics.(in preparation)
N.R. Nene, A. Zaikin. Gene regulatory network attractor selection and cell fate decision: insights into cancer multi-targeting. Proceedings of the BIOSIGNAL 2010 conference. 14th – 16th July 2010 Berlin, Germany

 

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