From Cold to Hot: Changing Perceptions and Future Opportunities for Quantitative Systems Pharmacology Modeling in Cancer Immunotherapy.

Immuno-oncology (IO) is a fast-expanding field due to recent success using IO therapies in treating cancer. As IO therapies do not directly kill tumor cells but rather act upon the patients' own immune cells either systemically or in the tumor microenvironment, new and innovative approaches are required to inform IO therapy research and development. Quantitative systems pharmacology (QSP) modeling describes the biological mechanisms of disease and the mode of action of drugs with mathematical equations, which has significant potential to address the big challenges in the IO field, from identifying patient populations that respond to different therapies to guiding the selection, dosing, and scheduling of combination therapy. To assess the perspectives of the community on the impact of QSP modeling in IO drug development and to understand current applications and challenges, the IO QSP working group-under the QSP Special Interest Group (SIG) of the International Society of Pharmacometrics (ISoP)-conducted a survey among QSP modelers, non-QSP modelers, and non-modeling IO program stakeholders. The survey results are presented here with discussions on how to address some of the findings. One of the findings is the differences in perception among these groups. To help bridge this perception gap, we present several case studies demonstrating the impact of QSP modeling in IO and suggest actions that can be taken in the future to increase the real and perceived impact of QSP modeling in IO drug research and development.

Pharmacology-based ranking of anti-cancer drugs to guide clinical development of cancer immunotherapy combinations.

The success of antibodies targeting Programmed cell death protein 1 (PD-1) and its ligand L1 (PD-L1) in cancer treatment and the need for improving response rates has led to an increased demand for the development of combination therapies with anti-PD-1/PD-L1 blockers as a backbone. As more and more drugs with translational potential are identified, the number of clinical trials evaluating combinations has increased considerably and the demand to prioritize combinations having potential for success over the ones that are unlikely to be successful is rising. This review aims to address the unmet need to prioritize cancer immunotherapy combinations through comprehensive search of potential drugs and ranking them based on their mechanism of action, clinical efficacy and safety. As lung cancer is one of the most frequently studied cancer types, combinations that showed potential for the treatment of lung cancer were prioritized. A literature search was performed to identify drugs with potential in combination with PD-1/PD-L1 blockers and the drugs were ranked based on their mechanism of action and known clinical efficacy. Nineteen drugs or drug classes were identified from an internal list of lead molecules and were scored for their clinical potential. Efficacy and safety data from pivotal studies was summarized for the selected drugs. Further, overlap of mechanisms of action and adverse events was visualized using a heat map illustration to help screen drugs for combinations. The quantitative scoring methodology provided in this review could serve as a template for preliminary ranking of novel combinations.

Structure-Dependent Chiroptical Properties of Twisted Multilayered Silver Nanowire Assemblies.

The optical properties of chiral plasmonic metasurfaces depend strongly on their architecture, in particular the orientation and spacing between the individual building blocks assembled into large arrays. However, methods to obtain chiral metamaterials with fully tunable chiroptical properties in the UV, visible, and near-infrared range are scarce. Here, we show that the chiroptical properties of silver nanowires assembled in helical nanostructures by grazing incidence spraying and Layer-by-Layer assembly can be finely tuned over a broad wavelength range using simple design principles. The angle between the oriented nanowire layers controls the intensity of the circular dichroism, reaching ellipticity values higher than 13° and g-factor values up to 1.6, while the shape of the circular dichroism spectra depends strongly on the spacing between the layers which can be tuned at the nanometer scale. The structure-dependent optical properties of the assembly are successfully modeled using a transfer matrix approach.

Nanoscale Bouligand Multilayers: Giant Circular Dichroism of Helical Assemblies of Plasmonic 1D Nano-Objects.

Chirality is found at all length scales in nature, and chiral metasurfaces have recently attracted attention due to their exceptional optical properties and their potential applications. Most of these metasurfaces are fabricated by top-down methods or bottom-up approaches that cannot be tuned in terms of structure and composition. By combining grazing incidence spraying of plasmonic nanowires and nanorods and Layer-by-Layer assembly, we show that nonchiral 1D nano-objects can be assembled into scalable chiral Bouligand nanostructures whose mesoscale anisotropy is controlled with simple macroscopic tools. Such multilayer helical assemblies of linearly oriented nanowires and nanorods display very high circular dichroism up to 13 000 mdeg and giant dissymmetry factors up to g ≈ 0.30 over the entire visible and near-infrared range. The chiroptical properties of the chiral multilayer stack are successfully modeled using a transfer matrix formalism based on the experimentally determined properties of each individual layer. The proposed approach can be extended to much more elaborate architectures and gives access to template-free and enantiomerically pure nanocomposites whose structure can be finely tuned through simple design principles.

Tuning the Chiroptical Properties of Elongated Nano-objects via Hierarchical Organization.

Chiral materials appear as excellent candidates to control and manipulate the polarization of light in optical devices. In nanophotonics, the self-assembly of colloidal plasmonic nanoparticles gives rise to strong resonances in the visible range, and when such organizations are chiral, a strong chiroplasmonic effect can be observed. In the present work, we describe the optical properties of chiral artificial nanophotonic materials, Goldhelices, which are hierarchically organized by grazing incidence spraying. These Goldhelices are made by plasmonic nanoparticles (gold) grafted onto helical templates made from silica nanohelices. A comparison of oriented versus non-oriented surfaces has been performed by Mueller matrix polarimetry, showing the importance of the organization of the Goldhelices regarding their interaction with light. Moreover, mono- versus multilayer photonic films are created, and the measured optical properties are discussed and compared to simulations.

Dynamics of Bone Cell Interactions and Differential Responses to PTH and Antibody-Based Therapies.

We propose a mathematical model describing the dynamics of osteoblasts and osteoclasts in bone remodeling. The goal of this work is to develop an integrated modeling framework for bone remodeling and bone cell signaling dynamics that could be used to explore qualitatively combination treatments for osteoporosis in humans. The model has been calibrated using 57 checks from the literature. Specific global optimization methods based on qualitative objectives have been developed to perform the model calibration. We also added pharmacokinetics representations of three drugs to the model, which are teriparatide (PTH(1-34)), denosumab (a RANKL antibody) and romosozumab (a sclerostin antibody), achieving excellent goodness-of-fit of human clinical data. The model reproduces the paradoxical effects of PTH on the bone mass, where continuous administration of PTH results in bone loss but intermittent administration of PTH leads to bone gain, thus proposing an explanation of this phenomenon. We used the model to simulate different categories of osteoporosis. The main attributes of each disease are qualitatively well captured by the model, for example changes in bone turnover in the disease states. We explored dosing regimens for each disease based on the combination of denosumab and romosozumab, identifying adequate ratios and doses of both drugs for subpopulations of patients in function of categories of osteoporosis and the degree of severity of the disease.

Analysis of the IJCNN 2011 UTL challenge.

We organized a challenge in "Unsupervised and Transfer Learning": the UTL challenge (http://clopinet.com/ul). We made available large datasets from various application domains: handwriting recognition, image recognition, video processing, text processing, and ecology. The goal was to learn data representations that capture regularities of an input space for re-use across tasks. The representations were evaluated on supervised learning "target tasks" unknown to the participants. The first phase of the challenge was dedicated to "unsupervised transfer learning" (the competitors were given only unlabeled data). The second phase was dedicated to "cross-task transfer learning" (the competitors were provided with a limited amount of labeled data from "source tasks", distinct from the "target tasks"). The analysis indicates that learned data representations yield significantly better results than those obtained with original data or data preprocessed with standard normalizations and functional transforms.

Free flaps for pressure sore coverage.

Management of pressure sores still represents a major challenge in plastic surgery practice due to recurrence. The surgeon may have to face multiple or recurrent pressure ulcerations without any local flap left. In this very limited indication, free flap surgery appears to be a useful adjunct in the surgical treatment. We reviewed our charts looking for patients operated for a pressure sore of the sacral, ischial, or trochanteric region. We found 88 consecutive patients representing 108 different pressure sores and 141 flap procedures. Among these patients, 6 presented large sores that could not be covered with a pedicled flap and benefited from free flap surgery (4.2% of all procedures). Stable coverage was achieved in 80% of these patients after a mean follow-up of 32 months. Comparison between pedicled and free flaps groups showed a trend in the latest concerning the presence of diabetes, incontinence, paraplegia, and male sex.

Sequential recruitment and combinatorial assembling of multiprotein complexes in transcriptional activation.

In human cells, estrogenic signals induce cyclical association and dissociation of specific proteins with the DNA in order to activate transcription of estrogen-responsive genes. These oscillations can be modeled by assuming a large number of sequential reactions represented by linear kinetics with random kinetic rates. Application of the model to experimental data predicts robust binding sequences in which proteins associate with the DNA at several different phases of the oscillation. Our methods circumvent the need to derive detailed kinetic graphs, and are applicable to other oscillatory biological processes involving a large number of sequential steps.

Modeling the interactions between osteoblast and osteoclast activities in bone remodeling.

We propose a mathematical model explaining the interactions between osteoblasts and osteoclasts, two cell types specialized in the maintenance of the bone integrity. Bone is a dynamic, living tissue whose structure and shape continuously evolves during life. It has the ability to change architecture by removal of old bone and replacement with newly formed bone in a localized process called remodeling. The model described here is based on the idea that the relative proportions of immature and mature osteoblasts control the degree of osteoclastic activity. In addition, osteoclasts control osteoblasts differentially depending on their stage of differentiation. Despite the tremendous complexity of the bone regulatory system and its fragmentary understanding, we obtain surprisingly good correlations between the model simulations and the experimental observations extracted from the literature. The model results corroborate all behaviors of the bone remodeling system that we have simulated, including the tight coupling between osteoblasts and osteoclasts, the catabolic effect induced by continuous administration of PTH, the catabolic action of RANKL, as well as its reversal by soluble antagonist OPG. The model is also able to simulate metabolic bone diseases such as estrogen deficiency, vitamin D deficiency, senescence and glucocorticoid excess. Conversely, possible routes for therapeutic interventions are tested and evaluated. Our model confirms that anti-resorptive therapies are unable to partially restore bone loss, whereas bone formation therapies yield better results. The model enables us to determine and evaluate potential therapies based on their efficacy. In particular, the model predicts that combinations of anti-resorptive and anabolic therapies provide significant benefits compared with monotherapy, especially for certain type of skeletal disease. Finally, the model clearly indicates that increasing the size of the pool of preosteoblasts is an essential ingredient for the therapeutic manipulation of bone formation. This model was conceived as the first step in a bone turnover modeling platform. These initial modeling results are extremely encouraging and lead us to proceed with additional explorations into bone turnover and skeletal remodeling.

New approach to vascular injection in fresh cadaver dissection.

Vascular injection techniques for anatomic studies are often complementary. Use of colored gelatinous mixtures with methylene blue provides precious data about descriptive anatomy by the contrast that it produces in the tissues. The introduction of radiopaque medium, such as lead oxide, into the gelatinous mixture can be used as a complement by means of x-ray examination, in order to facilitate and to reduce the time of investigation. Addition of rhodamine B to the radiopaque mixture keeps the advantages of the contrast medium, but also permits further dissection to demonstrate some details shown by prior x-ray examination. This article compares these different injection techniques in the study of the nasal vascular network. Moreover, it depicts a new injection approach that allows the investigation of vascular territories depending on thin caliber arteries by selective reinjection, defining microangiosomes. Each above-cited technique was used in ten facial territories of fresh cadavers. The patterns of the vessels shown by these techniques were identical, with a constant visualization of infra-millimetric arteries. However, selective reinjection was the only method that permitted characterization of the proper vascular territory of the lateral nasal artery.

Spatial effects in modeling pharmacokinetics of rapid action drugs.

We develop a model to describe the time course of plasma concentration of neuromuscular blocking agents used as anesthetics during surgery. This model, which overcomes the limitations of the classical compartment models routinely used in pharmacokinetics, incorporates spatial effects due to heterogeneity in the circulation: it takes the form of a dispersion equation on a circular domain, with a time-dependent leakage term. This term is fitted to the functional form desired once first-stage transients have died out. Comparisons are made with clinical data by adjusting three parameters in the model.