AUTHOR=Martínez-Méndez David , Villarreal Carlos , Huerta Leonor 

TITLE=Modeling uncertainty: the impact of noise in T cell differentiation

JOURNAL=Frontiers in Systems Biology

VOLUME=4

YEAR=2024

URL=https://www.frontiersin.org/journals/systems-biology/articles/10.3389/fsysb.2024.1412931

DOI=10.3389/fsysb.2024.1412931

ISSN=2674-0702

ABSTRACT=<sec><title>Background</title><p>The regulatory mechanisms guiding CD4 T cell differentiation are complex and are further influenced by intrinsic cell variability along with that of microenvironmental cues, such as cytokine and nutrient availability.</p></sec><sec><title>Objective</title><p>This study aims to expand our understanding of CD4 T cell differentiation by examining the influence of intrinsic noise on cell fate.</p></sec><sec><title>Methodology</title><p>A model based on a complex regulatory network of early signaling events involved in CD4 T cell activation and differentiation was described in terms of a set of stochastic differential equation to assess the effect of noise intensity on differentiation efficiency to the Th1, Th2, Th17, Treg, and <inline-formula id="inf1"><mml:math id="m1" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msub><mml:mrow><mml:mtext>T</mml:mtext></mml:mrow><mml:mrow><mml:mi>F</mml:mi><mml:mi>H</mml:mi></mml:mrow></mml:msub></mml:math></inline-formula> effector phenotypes under defined cytokine and nutrient conditions.</p></sec><sec><title>Results</title><p>The increase of noise intensity decreases differentiation efficiencies. In a microenvironment of Th1-inducing cytokines and optimal nutrient conditions, noise levels of 3<inline-formula id="inf2"><mml:math id="m2" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>%</mml:mi></mml:math></inline-formula>, 5<inline-formula id="inf3"><mml:math id="m3" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>%</mml:mi></mml:math></inline-formula> and 10<inline-formula id="inf4"><mml:math id="m4" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>%</mml:mi></mml:math></inline-formula> render Th1 differentiation efficiencies of 0.87, 0.76 and 0.62, respectively, underscoring the sensitivity of the network to random variations. Further increments of noise reveal that the network is relatively stable until noise levels of 20<inline-formula id="inf5"><mml:math id="m5" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>%</mml:mi></mml:math></inline-formula>, where the resulting cell phenotypes becomes heterogeneous. Notably, Treg differentiation showed the highest robustness to noise perturbations. A combined Th1-Th2 cytokine environment with optimal nutrient levels induces a dominant Th1 phenotype; however, removal of glutamine shifts the balance towards the Th2 phenotype at all noise levels, with an efficiency similar to that obtained under Th2-only cytokine conditions. Similarly, combinations of Th1/Treg and Treg/Th17-inducing cytokines along with the removal of either tryptophan or oxygen shift the dominant Th1 and Treg phenotypes towards Treg and Th17 respectively. Model results are consistent with differentiation efficiency patterns obtained under well-controlled experimental settings reported in the literature.</p></sec><sec><title>Conclusion</title><p>The stochastic CD4 T cell mathematical model presented here demonstrates a noise-dependent modulation of T cell differentiation induced by cytokines and nutrient availability. Modeling results can be explained by the network topology, which assures that the system will arrive at stable states of cell functionality despite variable levels of biological intrinsic noise. Moreover, the model provides insights into the robustness of the T cell differentiation process.</p></sec>