@article{talkington_mcsweeney_wessler_rath_li_zhang_yuan_frank_forest_cao_et al._2022, title={A PBPK model recapitulates early kinetics of anti-PEG antibody-mediated clearance of PEG-liposomes}, volume={343}, ISSN={["1873-4995"]}, DOI={10.1016/j.jconrel.2022.01.022}, abstractNote={PEGylation is routinely used to extend the systemic circulation of various protein therapeutics and nanomedicines. Nonetheless, mounting evidence is emerging that individuals exposed to select PEGylated therapeutics can develop antibodies specific to PEG, i.e., anti-PEG antibodies (APA). In turn, APA increase both the risk of hypersensitivity to the drug as well as potential loss of efficacy due to accelerated blood clearance of the drug. Despite the broad implications of APA, the timescales and systemic specificity by which APA can alter the pharmacokinetics and biodistribution of PEGylated drugs remain not well understood. Here, we developed a physiologically based pharmacokinetic (PBPK) model designed to resolve APA's impact on both early- and late-phase pharmacokinetics and biodistribution of intravenously administered PEGylated drugs. Our model accurately recapitulates PK and biodistribution data obtained from PET/CT imaging of radiolabeled PEG-liposomes and PEG-uricase in mice with and without APA, as well as serum levels of PEG-uricase in humans. Our work provides another illustration of the power of high-resolution PBPK models for understanding the pharmacokinetic impacts of anti-drug antibodies and the dynamics with which antibodies can mediate clearance of foreign species.}, journal={JOURNAL OF CONTROLLED RELEASE}, author={Talkington, Anne M. and McSweeney, Morgan D. and Wessler, Timothy and Rath, Marielle K. and Li, Zibo and Zhang, Tao and Yuan, Hong and Frank, Jonathan E. and Forest, M. Gregory and Cao, Yanguang and et al.}, year={2022}, month={Mar}, pages={518–527} }
 @article{talkington_wessler_lai_cao_forest_2021, title={Experimental Data and PBPK Modeling Quantify Antibody Interference in PEGylated Drug Carrier Delivery}, volume={83}, ISSN={["1522-9602"]}, DOI={10.1007/s11538-021-00950-z}, abstractNote={Physiologically-based pharmacokinetic (PBPK) modeling is a popular drug development tool that integrates physiology, drug physicochemical properties, preclinical data, and clinical information to predict drug systemic disposition. Since PBPK models seek to capture complex physiology, parameter uncertainty and variability is a prevailing challenge: there are often more compartments (e.g., organs, each with drug flux and retention mechanisms, and associated model parameters) than can be simultaneously measured. To improve the fidelity of PBPK modeling, one approach is to search and optimize within the high-dimensional model parameter space, based on experimental time-series measurements of drug distributions. Here, we employ Latin Hypercube Sampling (LHS) on a PBPK model of PEG-liposomes (PL) that tracks biodistribution in an 8-compartment mouse circulatory system, in the presence (APA+) or absence (naïve) of anti-PEG antibodies (APA). Near-continuous experimental measurements of PL concentration during the first hour post-injection from the liver, spleen, kidney, muscle, lung, and blood plasma, based on PET/CT imaging in live mice, are used as truth sets with LHS to infer optimal parameter ranges for the full PBPK model. The data and model quantify that PL retention in the liver is the primary differentiator of biodistribution patterns in naïve versus APA+ mice, and spleen the secondary differentiator. Retention of PEGylated nanomedicines is substantially amplified in APA+ mice, likely due to PL-bound APA engaging specific receptors in the liver and spleen that bind antibody Fc domains. Our work illustrates how applying LHS to PBPK models can further mechanistic understanding of the biodistribution and antibody-mediated clearance of specific drugs.}, number={12}, journal={BULLETIN OF MATHEMATICAL BIOLOGY}, author={Talkington, Anne M. and Wessler, Timothy and Lai, Samuel K. and Cao, Yanguang and Forest, M. Gregory}, year={2021}, month={Dec} }
 @article{schroeder_newby_schaefer_subramani_tubbs_gregory forest_miao_lai_2020, title={LPS-binding IgG arrests actively motile Salmonella Typhimurium in gastrointestinal mucus}, volume={13}, ISSN={["1935-3456"]}, DOI={10.1038/s41385-020-0267-9}, abstractNote={The gastrointestinal (GI) mucosa is coated with a continuously secreted mucus layer that serves as the first line of defense against invading enteric bacteria. We have previously shown that antigen-specific immunoglobulin G (IgG) can immobilize viruses in both human airway and genital mucus secretions through multiple low-affinity bonds between the array of virion-bound IgG and mucins, thereby facilitating their rapid elimination from mucosal surfaces and preventing mucosal transmission. Nevertheless, it remains unclear whether weak IgG-mucin crosslinks could reinforce the mucus barrier against the permeation of bacteria driven by active flagella beating, or in predominantly MUC2 mucus gel. Here, we performed high-resolution multiple particle tracking to capture the real-time motion of hundreds of individual fluorescent Salmonella Typhimurium in fresh, undiluted GI mucus from Rag1-/- mice, and analyzed the motion using a hidden Markov model framework. In contrast to control IgG, the addition of anti-lipopolysaccharide IgG to GI mucus markedly reduced the progressive motility of Salmonella by lowering the swim speed and retaining individual bacteria in an undirected motion state. Effective crosslinking of Salmonella to mucins was dependent on Fc N-glycans. Our findings implicate IgG-mucin crosslinking as a broadly conserved function that reduces mucous penetration of both bacterial and viral pathogens.}, number={5}, journal={MUCOSAL IMMUNOLOGY}, author={Schroeder, Holly A. and Newby, Jay and Schaefer, Alison and Subramani, Babu and Tubbs, Alan and Gregory Forest, M. and Miao, Ed and Lai, Samuel K.}, year={2020}, month={Sep}, pages={814–823} }
 @article{gasior_forest_gladfelter_newby_2020, title={Modeling the Mechanisms by Which Coexisting Biomolecular RNA-Protein Condensates Form}, volume={82}, ISSN={["1522-9602"]}, DOI={10.1007/s11538-020-00823-x}, abstractNote={Liquid-liquid phase separation is an emerging mechanism for intracellular organization. This work presents a mathematical model to examine molecular mechanisms that yield phase-separated droplets composed of different RNA-protein complexes. Using a Cahn-Hilliard diffuse interface model with a Flory-Huggins free energy scheme, we explore how multiple (here two, for simplicity) protein-RNA complexes (species) can establish a heterogeneous droplet field where droplets with single or multiple species phase separate and evolve during coarsening. We show that the complex-complex de-mixing energy tunes whether the complexes co-exist or form distinct droplets, while the transient binding kinetics dictate both the timescale of droplet formation and whether distinct species phase separate into droplets simultaneously or sequentially. For specific energetics and kinetics, a field of droplets driven by the formation of only one protein-RNA complex will emerge. Slowly, the other droplet species will accumulate inside the preformed droplets of the other species, allowing them to occupy the same droplet space. Alternatively, unfavorable species mixing creates a parasitic relationship: the slow-to-form protein-RNA complex will accumulate at the surface of a competing droplet species, siphoning off the free protein as it is released. Once this competing protein-RNA complex has sufficiently accumulated on the droplet surface, it can form a new droplet that is capable of sharing an interface with the first complex droplet but is not capable of mixing. These results give insights into a wide range of phase-separation scenarios and heterogeneous droplets that coexist but do not mix within the nucleus and the cytoplasm of cells.}, number={12}, journal={BULLETIN OF MATHEMATICAL BIOLOGY}, author={Gasior, K. and Forest, M. G. and Gladfelter, A. S. and Newby, J. M.}, year={2020}, month={Dec} }
 @article{mclaughlin_langdon_crutchley_holt_forest_newby_gladfelter_2020, title={Spatial heterogeneity of the cytosol revealed by machine learning-based 3D particle tracking}, volume={31}, ISSN={["1939-4586"]}, DOI={10.1091/mbc.E20-03-0210}, abstractNote={The structure of the cytosol across different length scales is a debated topic in cell biology. Here we present tools to measure the physical state of the cytosol by analyzing the 3D motion of nanoparticles expressed in cells. We find evidence that the physical structure of the cytosol is a fundamental source of variability in biological systems.}, number={14}, journal={MOLECULAR BIOLOGY OF THE CELL}, author={McLaughlin, Grace A. and Langdon, Erin M. and Crutchley, John M. and Holt, Liam J. and Forest, M. Gregory and Newby, Jay M. and Gladfelter, Amy S.}, year={2020}, month={Jul}, pages={1498–1511} }
 @article{xu_newby_schiller_schroeder_wessler_chen_forest_lai_2019, title={Modeling Barrier Properties of Intestinal Mucus Reinforced with IgG and Secretory IgA against Motile Bacteria}, volume={5}, ISSN={["2373-8227"]}, DOI={10.1021/acsinfecdis.9b00109}, abstractNote={The gastrointestinal (GI) tract is lined with a layer of viscoelastic mucus gel, characterized by a dense network of entangled and cross-linked mucins together with an abundance of antibodies (Ab). Secretory IgA (sIgA), the predominant Ab isotype in the GI tract, is a dimeric molecule with 4 antigen-binding domains capable of inducing efficient clumping of bacteria, or agglutination. IgG, another common Ab at mucosal surfaces, can cross-link individual viruses to the mucin mesh through multiple weak bonds between IgG-Fc and mucins, a process termed muco-trapping. Relative contributions by agglutination versus muco-trapping in blocking permeation of motile bacteria through mucus remain poorly understood. Here, we developed a mathematical model that takes into account physiologically relevant spatial dimensions and time scales, binding and unbinding rates between Ab and bacteria as well as between Ab and mucins, the diffusivities of Ab, and run-tumble motion of active bacteria. Our model predicts both sIgA and IgG can accumulate on the surface of individual bacteria at sufficient quantities and rates to enable trapping individual bacteria in mucins before they penetrate the mucus layer. Furthermore, our model predicts that agglutination only modestly improves the ability for antibodies to block bacteria permeation through mucus. These results suggest that while sIgA is the most potent Ab isotype overall at stopping bacterial penetration, IgG may represent a practical alternative for mucosal prophylaxis and therapy. Our work improves the mechanistic understanding of Ab-enhanced barrier properties of mucus and highlights the ability for muco-trapping Ab to protect against motile pathogens at mucosal surfaces.}, number={9}, journal={ACS INFECTIOUS DISEASES}, author={Xu, Feifei and Newby, Jay M. and Schiller, Jennifer L. and Schroeder, Holly A. and Wessler, Timothy and Chen, Alex and Forest, M. Gregory and Lai, Samuel K.}, year={2019}, month={Sep}, pages={1570–1580} }
 @article{gasior_zhao_mclaughlin_forest_gladfelter_newby_2019, title={Partial demixing of RNA-protein complexes leads to intradroplet patterning in phase-separated biological condensates}, volume={99}, ISSN={["2470-0053"]}, DOI={10.1103/PhysRevE.99.012411}, abstractNote={An emerging mechanism for intracellular organization is liquid-liquid phase separation (LLPS). Found in both the nucleus and the cytoplasm, liquidlike droplets condense to create compartments that are thought to promote and inhibit specific biochemistry. In this work, a multiphase, Cahn-Hilliard diffuse interface model is used to examine RNA-protein interactions driving LLPS. We create a bivalent system that allows for two different species of protein-RNA complexes and model the competition that arises for a shared binding partner, free protein. With this system we demonstrate that the binding and unbinding of distinct RNA-protein complexes leads to diverse spatial pattern formation and dynamics within droplets. Both the initial formation and transient behavior of spatial patterning are subject to the exchange of free proteins between RNA-protein complexes. This study illustrates that spatiotemporal heterogeneity can emerge within phase-separated biological condensates with simple binding reactions and competition. Intradroplet patterning may influence droplet composition and, subsequently, cellular organization on a larger scale.}, number={1}, journal={PHYSICAL REVIEW E}, author={Gasior, Kelsey and Zhao, Jia and McLaughlin, Grace and Forest, M. Gregory and Gladfelter, Amy S. and Newby, Jay}, year={2019}, month={Jan} }
 @article{chen_mckinley_wang_shi_mucha_forest_lai_2014, title={Transient Antibody-Mucin Interactions Produce a Dynamic Molecular Shield against Viral Invasion}, volume={106}, ISSN={["1542-0086"]}, DOI={10.1016/j.bpj.2014.02.038}, abstractNote={Given the difficulty in finding a cure for HIV/AIDS, a promising prevention strategy to reduce HIV transmission is to directly block infection at the portal of entry. The recent Thai RV144 trial offered the first evidence that an antibody-based vaccine may block heterosexual HIV transmission. Unfortunately, the underlying mechanism(s) for protection remain unclear. Here we theoretically examine a hypothesis that builds on our recent laboratory observation: virus-specific antibodies (Ab) can trap individual virions in cervicovaginal mucus (CVM), thereby reducing infection in vivo. Ab are known to have a weak-previously considered inconsequential-binding affinity with the mucin fibers that constitute CVM. However, multiple Ab can bind to the same virion at the same time, which markedly increases the overall Ab-mucin binding avidity, and creates an inheritable virion-mucin affinity. Our model takes into account biologically relevant length and timescales, while incorporating known HIV-Ab affinity and the respective diffusivities of viruses and Ab in semen and CVM. The model predicts that HIV-specific Ab in CVM leads to rapid formation and persistence of an HIV concentration front near the semen/CVM interface, far from the vaginal epithelium. Such an HIV concentration front minimizes the flux of HIV virions reaching target cells, and maximizes their elimination upon drainage of genital secretions. The robustness of the result implies that even exceedingly weak Ab-mucin affinity can markedly reduce the flux of virions reaching target cells. Beyond this specific application, the model developed here is adaptable to other pathogens, mucosal barriers, and geometries, as well as kinetic and diffusional effects, providing a tool for hypothesis testing and producing quantitative insights into the dynamics of immune-mediated protection.}, number={9}, journal={BIOPHYSICAL JOURNAL}, author={Chen, Alex and McKinley, Scott A. and Wang, Simi and Shi, Feng and Mucha, Peter J. and Forest, M. Gregory and Lai, Samuel K.}, year={2014}, month={May}, pages={2028–2036} }