Interpolation Methods for Molecular Potential Energy Surface Construction

The concept of a potential energy surface (PES) is one of the most important concepts in modern chemistry. A PES represents the relationship between the chemical system's energy and its geometry (i.e., atom positions) and can provide useful information about the system's chemical properties and reactivity. Construction of accurate PESs with high-level theoretical methodologies, such as density functional theory, is still challenging due to a steep increase in the computational cost with the increase of the system size. Thus, over the past few decades, many different mathematical approaches have been applied to the problem of the cost-efficient PES construction. This article serves as a short overview of interpolative methods for the PES construction, including global polynomial interpolation, trigonometric interpolation, modified Shepard interpolation, interpolative moving least-squares, and the automated PES construction derived from these.

779 Inhibiting type-I interferon signaling promotes memory T-cell formation following immunization with Listeria anti-cancer vaccines

Background

The aspiration of cancer immunotherapy is to generate large numbers of highly functional anti-tumor CD8+ T-cells. We and others have optimized Listeria monocytogenes as a powerful anti-cancer vaccine platform to drive such T-cell responses. Early clinical trial data suggest the number of T-cells generated correlates with efficacy, demanding an understanding of the factors that dictate vaccine-induced T-cell responses. The CD8+ T-cell response is intimately linked to magnitude and quality of the innate immune response triggered by vaccines. Listeria-based vaccines activate numerous innate pathways and can be engineered to hyper- or hypo-induce these pathways. We sought to understand how modulating innate immunity would impact vaccine efficacy.

Methods

To dissect the impact of type I interferon signaling and the inflammasomes on L. monocytogenes induced T-cell responses, we immunized IFNAR-/-, Caspase1/11-/-, and novel IFNAR-/-Caspase1/11-/- double knockouts mice we generated for this study. CD8+ T-cell responses were assessed at the peak T-cell response, after contraction and memory formation, and after rechallenge. The phenotype and magnitude of CD8+ T-cells was assessed at each stage, and functional outcomes were assessed by measuring protection from reinfection by wild-type Listeria.

Results

IFNAR-/- mice developed the largest number of CD8+ T-cells during the peak primary response contradicting the dogma that Type-I Interferon promotes robust CD8+ T-cell responses. Caspase1/11-/- mice were not significantly different from wild-type mice. The frequency of short-lived effector cells (assessed by expression of CD127 and KLRG1) was no different between wild-type and IFNAR-/- mice, however we observed more than twice as many memory precursor cells at the peak CD8+ T-cell response. These findings extend to the memory and recall stage with more antigen-specific T-cells observed after contraction and upon rechallenge. Finally, IFNAR-/- mice are remarkably more protected from wild-type Listeria rechallenge than their counterparts after immunization demonstrating the efficacy of the increased memory T-cell pool. Data are representative of at least two independent replicates with at least 5 mice per group and significance was assessed by one-way ANOVA with *p<0.05.

Conclusions

We demonstrated that type-I interferon signaling deficiency leads to enhanced prophylactic vaccine efficacy through increased memory T-cell formation. Ultimately, for patients with slow growing tumors or with high-risk mutations, prophylactic tumor vaccines could elicit life-long protection from disease. Importantly, increased memory precursor T-cell abundance did not come at the expense of short-lived effectors leaving open the possibility that blocking Type-I IFN could potentiate lasting immunological memory in both the therapeutic and prophylactic setting.

A rare case of a novel coagulase negative Staphylococcus native valve endocarditis in a 28-year-old male

Coagulase negative staphylococci (CoNS) are an emerging cause of native valve endocarditis in community and healthcare settings. We describe a case of a 28-year-old man with no significant risk factors who presented with Staphylococcus pettenkoferi native valve endocarditis. During our patient’s initial hospitalization, he was treated for CoNS bacteraemia and subsequently discharged after a protracted hospital course with a transthoracic echocardiogram (TTE) showing no valvular vegetations. However, during the course of his second hospitalization, speciation identified S. pettenkoferi and transoesophageal echocardiogram (TEE) showed aortic valve perforations with new regurgitation raising concern for left sided endocarditis. We postulate that our patient may have been infected with the same CoNS species causing aortic valve endocarditis during his initial hospitalization. This case highlights the importance of recognizing CoNS as a possible causative bacterium in NVE, as well as the importance of obtaining a TEE when evaluating a patient for suspected endocarditis.

Reduced-dimensional surface hopping with offline-online computations

Molecular dynamics simulations often classically evolve the nuclear geometry on adiabatic potential energy surfaces (PESs), punctuated by random hops between energy levels in regions of strong coupling, in an algorithm known as surface hopping. However, the computational expense of integrating the geometry on a full-dimensional PES and computing the required couplings can quickly become prohibitive as the number of atoms increases. In this work, we describe a method for surface hopping that uses only important reaction coordinates, performs all expensive evaluations of the true PESs and couplings only once before simulating dynamics (offline), and then queries the stored values during the surface hopping simulation (online). Our Python codes are freely available on GitHub. Using photodissociation of azomethane as a test case, this method is able to reproduce experimental results that have thus far eluded ab initio surface hopping studies.

Efficient Approximation of Potential Energy Surfaces with Mixed-Basis Interpolation

The potential energy surface (PES) describes the energy of a chemical system as a function of its geometry and is a fundamental concept in modern chemistry. A PES provides much useful information about the system, including the structures and energies of various stationary points, such as stable conformers (local minima) and transition states (first-order saddle points) connected by a minimum-energy path. Our group has previously produced surrogate reduced-dimensional PESs using sparse interpolation along chemically significant reaction coordinates, such as bond lengths, bond angles, and torsion angles. These surrogates used a single interpolation basis, either polynomials or trigonometric functions, in every dimension. However, relevant molecular dynamics (MD) simulations often involve some combination of both periodic and nonperiodic coordinates. Using a trigonometric basis on nonperiodic coordinates, such as bond lengths, leads to inaccuracies near the domain boundary. Conversely, polynomial interpolation on the periodic coordinates does not enforce the periodicity of the surrogate PES gradient, leading to nonconservation of total energy even in a microcanonical ensemble. In this work, we present an interpolation method that uses trigonometric interpolation on the periodic reaction coordinates and polynomial interpolation on the nonperiodic coordinates. We apply this method to MD simulations of possible isomerization pathways of azomethane between cis and trans conformers. This method is the only known interpolative method that appropriately conserves total energy in systems with both periodic and nonperiodic reaction coordinates. In addition, compared to all-polynomial interpolation, the mixed basis requires fewer electronic structure calculations to obtain a given level of accuracy, is an order of magnitude faster, and is freely available on GitHub.

Abstract 5733: Versican proteolytic fragments (matrikines) synergize with STING agonists to elicit robust anti-tumor CD8+ T cell responses

The impact of tumor matrix remodeling to the generation of an “inflamed” microenvironment that modulates responses to immunotherapy is unclear. Versican (VCAN) is a chondroitin sulphate matrix proteoglycan that promotes tolerogenic polarization of intratumoral DC through Toll-like receptor 2 (TLR2). Proteolytic processing of VCAN releases a bioactive N-terminal fragment (matrikine), versikine. In contrast to the tolerogenic actions of parental VCAN, versikine triggers IRF8-dependent transcription in myeloid cells and promotes Batf3-dendritic cell (DC) generation from FLT3L-mobilized bone marrow progenitors in vitro. Consistent with the Batf3-promoting effects of versikine, VCAN proteolysis correlates with T-cell infiltration across multiple cancers.The aims were to 1. define the impact of versikine on the intratumoral myeloid repertoire in vivo and 2. to define the efficacy of versikine as a vaccine adjuvant.4T1 breast carcinoma and Lewis Lung Carcinoma (LLC) empty vector (EV)- and versikine-expressing cells were implanted subcutaneously in syngeneic recipients. 1000mm3 tumors were harvested and intratumoral DC subsets were enumerated. Versikine-expressing tumors were characterized by significantly enhanced Batf3-DC (CD11chigh,MHC IIhigh Ly6C-, CD64-, CD24high,CD11blow) (p =0.0079 for 4T1 model and &lt;0.0001 for LLC model), whereas cDC2 (CD11chigh,MHC IIhigh Ly6C-, CD64-, CD24low, CD11bhigh ) frequency was diminished (p= 0.0079 and &lt;0.0001 respectively). Monocytic-derived DC (Mo-DC: CD11chigh, MHC IIhigh, Ly6C+, CD64+) remained unchanged. To determine the impact of versikine on responses to in situ vaccination using STING agonists, EV- and versikine-replete tumors (B16 and 4T1; 150 mm3), were injected intratumorally (IT) with a single subtherapeutic dose (200 μg) of DMXAA (murine STING agonist) or vehicle. EV-tumors did not significantly respond to 200μg DMXAA, whereas many B16-versikine and 4T1-versikine tumors regressed or growth was inhibited (p&lt;0.001 and p=0.014 respectively). Necrosis was frequently observed in 4T1 versikine-secreting tumors (6/9 mice) within 24 hours after treatment. Versikine extended survival after subtherapeutic DMXAA treatment in 4T1; log rank=p=0.01. Versikine's effects were abrogated in Batf3-null mice. To quantitate antigen-specific responses in the presence or absence of versikine, EV- and versikine-replete LLC tumors were injected IT with 500 μg DMXAA (therapeutic dose) or vehicle. We observed a significant increase in the frequency of CD8+ MHCI:SIINFEKL tetramer+ splenocytes in LLC-versikine-bearing animals as well as a marked increase in central memory T splenocytes (TCM) (CD62LhighCD44high). VCAN matrikines may generate effective adjuvants for in situ vaccination strategies across diverse solid and hematopoietic tumor types.

Citation Format: Athanasios Papadas, Evan Flietner, Zachary Morrow, Joshua Wiesner, Alexander Cicala, Adam Pagenkopf, Chelsea Hope, Philip Emmerich, Dustin Deming, Jing Zhang, Peiman Hematti, Natalie Callander, Alexander Rakhmilevich, Mario Otto, Christian Capitini, Fotis Asimakopoulos. Versican proteolytic fragments (matrikines) synergize with STING agonists to elicit robust anti-tumor CD8+ T cell responses [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5733.

Approximating Periodic Potential Energy Surfaces with Sparse Trigonometric Interpolation

The potential energy surface (PES) describes the energy of a chemical system as a function of its geometry and is a fundamental concept in computational chemistry. A PES provides much useful information about the system, including the structures and energies of various stationary points, such as local minima, maxima, and transition states. Construction of full-dimensional PESs for molecules with more than 10 atoms is computationally expensive and often not feasible. Previous work in our group used sparse interpolation with polynomial basis functions to construct a surrogate reduced-dimensional PESs along chemically significant reaction coordinates, such as bond lengths, bond angles, and torsion angles. However, polynomial interpolation does not preserve the periodicity of the PES gradient with respect to angular components of geometry, such as torsion angles, which can lead to nonphysical phenomena. In this work, we construct a surrogate PES using trigonometric basis functions, for a system where the selected reaction coordinates all correspond to the torsion angles, resulting in a periodically repeating PES. We find that a trigonometric interpolation basis not only guarantees periodicity of the gradient but also results in slightly lower approximation error than polynomial interpolation.

Tumor matrix remodeling and novel immunotherapies: the promise of matrix-derived immune biomarkers

Recent advances in our understanding of the dynamics of cellular cross-talk have highlighted the significance of host-versus-tumor effect that can be harnessed with immune therapies. Tumors exploit immune checkpoints to evade adaptive immune responses. Cancer immunotherapy has witnessed a revolution in the past decade with the development of immune checkpoint inhibitors (ICIs), monoclonal antibodies against cytotoxic T lymphocyte antigen 4 (CTLA-4) and programmed cell death protein 1 (PD-1) or their ligands, such as PD1 ligand 1 (PD-L1). ICIs have been reported to have activity against a broad range of tumor types, in both solid organ and hematologic malignancy contexts. However, less than one-third of the patients achieve a durable and meaningful treatment response. Expression of immune checkpoint ligands (e.g., PD-L1), mutational burden and tumor-infiltrating lymphocytes are currently used as biomarkers for predicting response to ICIs. However, they do not reliably predict which patients will benefit from these therapies. There is dire need to discover novel biomarkers to predict treatment efficacy and to identify areas for development of combination strategies to improve response rates. Emerging evidence suggests key roles of tumor extracellular matrix (ECM) components and their proteolytic remodeling products in regulating each step of the cancer-immunity cycle. Here we review tumor matrix dynamics and matrix remodeling in context of anti-tumor immune responses and immunotherapy and propose the exploration of matrix-based biomarkers to identify candidates for immune therapy.