Dynamics of the activation of Lck

The enzyme Lck (lymphocyte-associated tyrosine kinase) is of central importance in the function of immune cells. I hope that mathematics can contribute to the understanding and improvement of immune checkpoint therapies for cancer. For this reason I have looked at the relevant mathematical models in the literature. In doing this I have realized the importance in this context of obtaining a better understanding of the activation of Lck. I was already familiar with the role of Lck in the activation of T cells. There are two tyrosines in Lck, Y394 and Y505, whose phosphorylation state influences its activity. Roughly speaking, phosphorylation of Y394 increases the activity of Lck while phosphorylation of Y505 decreases it. The fact that these are influences going in opposite directions already indicates complications. In fact the kinase Lck catalyses its own phosphorylation, especially on Y394. This is an example of autophosphorylation in trans, i.e. one molecule of Lck catalyses the phosphorylation of another molcule of Lck. It turns out that autophosphorylation tends to favour complicated dynamics. It is already the case that in a protein with a single phosphorylation site the occurrence of autophosphorylation can lead to bistability. Normally bistability in a chemical reaction network means the existence of more than one stable positive steady state and this is the definition I usually adopt. The definition may be weakened to the existence of more than one non-negative stable steady state. That autophosphorylation can produce bistability in this weaker sense was already observed by Lisman in 1985 (PNAS 82, 3055). He was interested in this as a mechanism of information storage in a biochemical system. In 2006 Fuss et al. (Bioinformatics 22, 158) found bistability in the strict sense in a model for the dynamics of Src kinases. Since Lck is a typical member of the family of Src kinases these results are also of relevance for Lck. In that work the phosphorylation processes are embedded in feedback loops. In fact the bistability is present without the feedback, as observed by Kaimachnikov and Kholodenko (FEBS J. 276, 4102). Finally, it was shown by Doherty et al. (J. Theor. Biol. 370, 27) that bistability (in the strict sense) can occur for a protein with only one phosphorylation site. This is in contrast to more commonly considered phosphorylation systems. These authors have also seen more complicated dynamical behaviour such as periodic solutions.

All these results on the properties of solutions of reaction networks are on the level of simulations. Recently Lisa Kreusser and I set out to investigate these phenomena on the level of rigorous mathematics and we have just put a paper on this subject on the archive. The model developed by Doherty et al. is one-dimensional and therefore relatively easy to analyse. The first thing we do is to give a rigorous proof of bistability for this system together with some information on the region of parameter space where this phenomenon occurs. We also show that it can be lifted to the system from which the one-dimensional system is obtained by timescale separation. The latter system has no periodic solutions. To obtain bistability the effect of the phosphorylation must be to activate the enzyme. It does not occur in the case of inhibition. We show that when an external kinase is included (in the case of Lck there is an external kinase Csk which may be relevant) and we do not restrict to the Michaelis-Menten regime bistability is restored.

We then go on to study the dynamics of the model of Kaimachnikov and Kholodenko, which is three-dimensional. These authors mention that it can be reduced to a two-dimensional model by timescale separation. Unfortunately we did not succeed in finding a rigorous framework for their reduction. Instead we used another related reduction which gives a setting which is well-behaved in the sense of geometric singular perturbation theory (normally hyperbolic) and can therefore be used to lift dynamical features from two to three dimensions in a rather straightforward way. It then remains to analyse the two-dimensonal system. It is easy to deduce bistability from the results already mentioned. We go further and show that there exist periodic and homoclinic solutions. This is done by showing the existence of a generic Bogdanov-Takens bifurcation, a procedure described more generally here and here. This system contains an abundance of parameters and the idea is to fix these so as to get the desired result. First we choose the coordinates of the steady state to be fixed simple rational numbers. Then we fix all but four of the parameters in the system. The four conditions for a BT bifurcation are then used to determine the values of the other four parameters. To get the desired positivity for the computed values the choices must be made carefully. This was done by trial and error. Establishing genericity required a calculation which was complicated but doable by hand. When a generic BT bifurcation has been obtained it follows that there are generic Hopf bifurcations nearby in parameter space and the nature of these (sub- or supercritical) can be determined. It turns out that in our case they are subcritical so that the associated periodic solutions are unstable. Having proved that periodic solutions exist we wanted to see what a solution of this type looks like by simulation. We had difficulties in finding parameter values for which this could be done. (We know the parameter values for the BT point and that those for the periodic solution are nearby but they must be chosen in a rather narrow region which we do not know explicitly.) Eventually we succeeded in doing this. In this context I used the program XPPAUT for the first time in my life and I learned to appreciate it. I see this paper as the beginning rather than the end of a path and I am very curious as to where it will lead.

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