A mechanistic systems pharmacology modeling platform to investigate the effect of PD-L1 expression heterogeneity and dynamics on the efficacy of PD-1 and PD-L1 blocking antibodies in cancer.

Tumors have developed multitude of ways to evade immune response and suppress cytotoxic T cells. Programed cell death protein 1 (PD-1) and programed cell death ligand 1 (PD-L1) are immune checkpoints that when activated, rapidly inactivate the cytolytic activity of T cells. Expression heterogeneity of PD-L1 and the surface receptor dynamics of both PD-1 and PD-L1 may be important parameters in modulating the immune response. PD-L1 is expressed on both tumor and non-tumor immune cells and this differential expression reflects different aspects of anti-tumor immunity. Here, we developed a mechanistic computational model to investigate the role of PD-1 and PD-L1 dynamics in modulating the efficacy of PD-1 and PD-L1 blocking antibodies. Our model incorporates immunological synapse restricted interaction of PD-1 and PD-L1, basal parameters for receptor dynamics, and T cell interaction with tumor and non-tumor immune cells. Simulations predict the existence of a threshold in PD-1 expression above which there is no efficacy for both anti-PD-1 and anti-PD-L1. Model also predicts that anti-tumor response is more sensitive to PD-L1 expression on non-tumor immune cells than tumor cells. New combination strategies are suggested that may enhance efficacy in resistant cases such as combining anti-PD-1 with a low dose of anti-PD-L1 or with inhibitors of PD-L1 recycling and synthesis. Another combination strategy suggested by the model is the combination of anti-PD-1 and anti-PD-L1 with enhancers of PD-L1 degradation rate. Virtual patients are then generated to test specific biomarkers of response. Intriguing predictions that emerge from the virtual patient simulations are that PD-1 blocking antibody results in higher response rate than PD-L1 blockade and that PD-L1 expression density on non-tumor immune cells rather than tumor cells is a predictor of response.

Investigating the pharmacodynamic durability of GalNAc-siRNA conjugates.

One hallmark of trivalent N-acetylgalactosamine (GalNAc)-conjugated siRNAs is the remarkable durability of silencing that can persist for months in preclinical species and humans. Here, we investigated the underlying biology supporting this extended duration of pharmacological activity. We found that siRNA accumulation and stability in acidic intracellular compartments is critical for long-term activity. We show that functional siRNA can be liberated from these compartments and loaded into newly generated Argonaute 2 protein complexes weeks after dosing, enabling continuous RNAi activity over time. Identical siRNAs delivered in lipid nanoparticles or as GalNAc conjugates were dose-adjusted to achieve similar knockdown, but only GalNAc-siRNAs supported an extended duration of activity, illustrating the importance of receptor-mediated siRNA trafficking in the process. Taken together, we provide several lines of evidence that acidic intracellular compartments serve as a long-term depot for GalNAc-siRNA conjugates and are the major contributor to the extended duration of activity observed in vivo.

Effects of Hierarchical Surface Roughness on Droplet Contact Angle.

Superhydrophobic surfaces often incorporate roughness on both micron and nanometer length scales, although a satisfactory understanding of the role of this hierarchical roughness in causing superhydrophobicity remains elusive. We present a two-dimensional thermodynamic model to describe wetting on hierarchically grooved surfaces by droplets for which the influence of gravity is negligible. By creating wetting phase diagrams for droplets on surfaces with both single-scale and hierarchical roughness, we find that hierarchical roughness leads to greatly expanded superhydrophobic domains in phase space over those for a single scale of roughness. Our results indicate that an important role of the nanoscale roughness is to increase the effective Young's angle of the microscale features, leading to smaller required aspect ratios (height to width) for the surface structures. We then show how this idea may be used to design a hierarchically rough surface with optimally high contact angles.

Kinetics of droplet wetting mode transitions on grooved surfaces: forward flux sampling.

The wetting configuration of a liquid droplet on a rough or physically patterned surface is typically characterized by either the Cassie wetting mode, in which the droplet resides on top of the roughness, or the Wenzel mode, in which the droplet penetrates into the roughness. For a fixed surface topology and droplet size, one of these modes corresponds to the global free-energy minimum. However, the other state is often metastable and long-lived due to a free-energy barrier that hinders the transition between the two wetting states. Metastable wetting states have been observed experimentally, and we also observe them in molecular dynamics (MD) simulations of a droplet on a grooved surface. Using forward flux sampling, we study the kinetics of the Cassie to Wenzel and Wenzel to Cassie transitions for two-dimensional droplets on periodically grooved substrates. The global-minimum wetting states that emerge from our nanoscale MD approach are consistent with those predicted by a macroscopic model based on free energy minimization. We find that the free-energy barriers for these transitions depend on the droplet size and surface topology. A committor analysis indicates that the transition-state ensemble consists of droplets that are on the verge of initiating/breaking contact with the substrate at the bottom of the grooves.

Wetting on physically patterned solid surfaces: the relevance of molecular dynamics simulations to macroscopic systems.

We used molecular dynamics (MD) simulations to study the wetting of Lennard-Jones cylindrical droplets on surfaces patterned with grooves. By scaling the surface topography parameters with the droplet size, we find that the preferred wetting modes and contact angles become independent of the droplet size. This result is in agreement with a mathematical model for the droplet free energy at small Bond numbers for which the effects of gravity are negligible. The MD contact angles for various wetting modes are in good agreement with those predicted by the mathematical model. We construct phase diagrams of the dependence of the wetting modes observed in the MD simulations on the topography of the surface. Depending on the topographical parameters characterizing the surface, multiple wetting modes can be observed, as is also seen experimentally. Thus, our studies indicate that MD simulations can yield insight into the large-length-scale behavior of droplets on patterned surfaces.

A theory for the morphological dependence of wetting on a physically patterned solid surface.

We present a theoretical model for predicting equilibrium wetting configurations of two-dimensional droplets on periodically grooved hydrophobic surfaces. The main advantage of our model is that it accounts for pinning/depinning of the contact line at step edges, a feature that is not captured by the Cassie and Wenzel models. We also account for the effects of gravity (via the Bond number) on various wetting configurations that can occur. Using free-energy minimization, we construct phase diagrams depicting the dependence of the wetting modes (including the number of surface grooves involved in the wetting configuration) and their corresponding contact angles on the geometrical parameters characterizing the patterned surface. In the limit of vanishing Bond number, the predicted wetting modes and contact angles become independent of drop size if the geometrical parameters are scaled with drop radius. Contact angles predicted by our continuum-level theoretical model are in good agreement with corresponding results from nanometer-scale molecular dynamics simulations. Our theoretical predictions are also in good agreement with experimentally measured contact angles of small drops, for which gravitational effects on interface deformation are negligible. We show that contact-line pinning is important for superhydrophobicity and that the contact angle is maximized when the droplet size is comparable to the length scale of the surface pattern.