Immunosurveillance shapes the emergence of neo-epitope landscapes of sarcomas, revealing prime targets for immunotherapy.

T cells recognize tumor-derived mutated peptides presented on MHC by tumors. The recognition of these neo-epitopes leads to rejection of tumors, an event that is critical for successful cancer immunosurveillance. Determination of tumor-rejecting neo-epitopes in human tumors has proved difficult, though recently developed systems approaches are becoming increasingly useful at evaluating their immunogenicity. We have used the differential aggretope index to determine the neo-epitope burden of sarcomas and observed a conspicuously titrated antigenic landscape, ranging from the highly antigenic osteosarcomas to the low antigenic leiomyosarcomas and liposarcomas. We showed that the antigenic landscape of the tumors inversely reflected the historical T cell responses in the tumor-bearing patients. We predicted that highly antigenic tumors with poor antitumor T cell responses, such as osteosarcomas, would be responsive to T cell-based immunotherapy regimens and demonstrated this in a murine osteosarcoma model. Our study presents a potentially novel pipeline for determining antigenicity of human tumors, provides an accurate predictor of potential neo-epitopes, and will be an important indicator of which cancers to target with T cell-enhancing immunotherapy.

Signatures of coherent vibronic exciton dynamics and conformational control in the two-dimensional electronic spectroscopy of conjugated polymers.

Two-dimensional electronic spectroscopy (2DES) signals for homo-oligomer J-aggregates are computed, with a focus on the role of structural change induced by low-frequency torsional modes, along with quasi-stationary trapping effects induced by high-frequency polaronic modes. To this end, a model system is derived from an ab initio parametrized site-based Hamiltonian for oligothiophenes [Binder et al., Phys. Rev. Lett., 2018, 120, 227401]. To obtain a compact representation, we introduce a collective lattice mode whose vibronic coupling depends nonlinearly on the exciton density. As a result, an N-site model with a single polaronic mode and a single torsional mode is obtained. Furthermore, a quantum-classical treatment is employed where the torsional mode is treated within a mean-field Ehrenfest/Langevin approximation. 2D electronic spectra are computed using the equation-of-motion phase-matching approach (EOM-PMA) within a wavefunction description. It is seen that the spectra combine the vibronic fine structure, due to the polaronic mode, and a dynamic Stokes shift, due to torsional relaxation. The signatures of the coherent effects and adiabatic evolution in the 2DES signals are discussed.

Agents of cancer immunosurveillance: HSPs and dsDNA.

Tumor immunosurveillance requires tumor cell-derived molecules to initiate responses through corresponding receptors on antigen presenting cells (APCs) and a specific effector response designed to eliminate the emerging tumor cells. This is supported by evidence from immunodeficient individuals and experimental animals. Recent discoveries suggest that adjuvanticity of tumor-derived heat shock proteins (HSPs) and double-stranded DNA (dsDNA) are necessary for tumor-specific immunity. There is also the obligatory early transfer of tumor antigens to APCs. We argue that tumor-derived HSPs deliver sufficient chaperoned antigen for cross-priming within the quantitative limits set by nascent tumors. In contrast to late-stage tumors, we are only just beginning to understand the unique interactions of the immune system with precancerous/nascent neoplastic cells, which is important for improved cancer prevention measures.

LCVM infection generates tumor antigen-specific immunity and inhibits growth of nonviral tumors.

Antibodies and T cells specific for tumor-associated antigens (TAA) are found in individuals without cancer but with a history of infections and are associated with lowered cancer risk. We hypothesized that those immune responses were generated to transiently abnormally expressed self-antigens on infected cells (disease-associated antigens, DAA) and later on tumor cells as TAA. We tested this hypothesis in mice with a history of infection with lymphocytic choriomeningitis virus (LCMV) Armstrong strain (Arm) that causes acute infection when injected intraperitoneally or CL-13 strain that establishes chronic infection when injected intravenously. Both elicited antibodies and T cells that recognized DAA/TAA on infected cells and on mouse tumors. When challenged with those tumors, Arm-experienced mice controlled tumors better than CL-13-experienced mice or infection-naïve mice. We characterized 7 DAA/TAA that were targets of LCMV-elicited antitumor immunity. We then vaccinated mice with tumor-derived gp96, a heat shock protein that binds a variety of TAA peptides, including those expressed on virus-infected cells as DAA. Tumor-gp96 vaccine induced DAA/TAA-specific immunity. When challenged with Cl-13, the mice showed lower viral copy numbers both early (day 7) and late (day 70) in infection. DAA/TAA may be immunogenic and safe candidates to develop vaccines to control both infections and cancer.

Aging-Associated Changes in the Adult Human Skin Microbiome and the Host Factors that Affect Skin Microbiome Composition.

Understanding the changes in the skin microbiome and their relationship to host skin factors during aging remains largely unknown. To better understand this phenomenon, we collected samples for metagenomic and host skin factor analyses from the forearm, buttock, and facial skin from 158 Caucasian females aged 20‒24, 30‒34, 40‒44, 50‒54, 60‒64, and 70‒74 years. Metagenomics analysis was performed using 16S ribosomal RNA gene sequencing, whereas host sebocyte gland area, skin lipids, natural moisturizing factors, and antimicrobial peptides measurements were also performed. These analyses showed that skin bacterial diversity increased at all the skin sites with increasing age. Of the bacterial genera with an average relative abundance >1%, only Lactobacillus and Cutibacterium demonstrated a significant change (decrease) in abundance at all sampled skin sites with increasing age. Additional bacterial genera demonstrated significant age- and site-specific changes in abundance. Analysis of sebocyte area, natural moisturizing factors, lipids, and antimicrobial peptides showed an age-related decrease in sebocyte area and increases in natural moisturizing factors/antimicrobial peptides/skin lipids, all of which correlated with changes in specific bacterial genera. In conclusion, the human skin microbiome undergoes age-associated alterations that may reflect underlying age-related changes in cutaneous biology.

Transcriptomic analysis of human skin wound healing and rejuvenation following ablative fractional laser treatment.

Ablative fractional laser treatment is considered the gold standard for skin rejuvenation. In order to understand how fractional laser works to rejuvenate skin, we performed microarray profiling on skin biopsies to identify temporal and dose-response changes in gene expression following fractional laser treatment. The backs of 14 women were treated with ablative fractional laser (Fraxel®) and 4 mm punch biopsies were collected from an untreated site and at the treated sites 1, 3, 7, 14, 21 and 28 days after the single treatment. In addition, in order to understand the effect that multiple fractional laser treatments have on skin rejuvenation, several sites were treated sequentially with either 1, 2, 3, or 4 treatments (with 28 days between treatments) followed by the collection of 4 mm punch biopsies. RNA was extracted from the biopsies, analyzed using Affymetrix U219 chips and gene expression was compared between untreated and treated sites. We observed dramatic changes in gene expression as early as 1 day after fractional laser treatment with changes remaining elevated even after 1 month. Analysis of individual genes demonstrated significant and time related changes in inflammatory, epidermal, and dermal genes, with dermal genes linked to extracellular matrix formation changing at later time points following fractional laser treatment. When comparing the age-related changes in skin gene expression to those induced by fractional laser, it was observed that fractional laser treatment reverses many of the changes in the aging gene expression. Finally, multiple fractional laser treatments, which cover different regions of a treatment area, resulted in a sustained or increased dermal remodeling response, with many genes either differentially regulated or continuously upregulated, supporting previous observations that maximal skin rejuvenation requires multiple fractional laser treatments. In conclusion, fractional laser treatment of human skin activates a number of biological processes involved in wound healing and tissue regeneration.

Tunable heat shock protein-mediated NK cell responses are orchestrated by STAT1 in Antigen Presenting Cells.

The release of Heat Shock Proteins (HSPs) from aberrant cells can initiate immune responses following engagement of the HSPs with antigen presenting cells (APCs). This is an important mechanism for cancer immunosurveillance and can also be modeled by vaccination with HSPs through various routes, targeting specific APCs expressing the HSP receptor CD91. Immunological outcomes can be varied as a result of the broad expression of CD91 in different dendritic cell and macrophage populations. We investigated the cellular response of different APCs to the prototypical immunogenic HSP, gp96, in the context of Th1 immunity. Although APCs generally express similar levels of the HSP receptor CD91, we uncovered APC-distinct, downstream signaling pathways activating STAT1, and differential STAT1 induced genes. As a result of this differential and unique signaling we determined that gp96-activated macrophages, but not DCs are capable of activating NK cells to produce IFN-[Formula: see text]. These data demonstrate that different APC subsets elicit unique intracellular signaling responses to HSPs which result in different patterns of downstream cellular activation and immune responses. Collectively this provides a novel tunable and autochthonous immune response to extracellular HSPs which has important implications on the development of immunity to cancer and infectious disease, as well as homeostasis.

Quantum Dynamics of Exciton Transport and Dissociation in Multichromophoric Systems.

Due to the subtle interplay of site-to-site electronic couplings, exciton delocalization, nonadiabatic effects, and vibronic couplings, quantum dynamical studies are needed to elucidate the details of ultrafast photoinduced energy and charge transfer events in organic multichromophoric systems. In this vein, we review an approach that combines first-principles parameterized lattice Hamiltonians with accurate quantum dynamical simulations using advanced multiconfigurational methods. Focusing on the elementary transfer steps in organic functional materials, we address coherent exciton migration and creation of charge transfer excitons in homopolymers, notably representative of the poly(3-hexylthiophene) material, as well as exciton dissociation at polymer:fullerene heterojunctions. We emphasize the role of coherent transfer, trapping effects due to high-frequency phonon modes, and thermal activation due to low-frequency soft modes that drive a diffusive dynamics.

Quantum dynamical simulations of intra-chain exciton diffusion in an oligo (para-phenylene vinylene) chain at finite temperature.

We report on quantum dynamical simulations of exciton diffusion in an oligo(para-phenylene vinylene) chain segment with 20 repeat units (OPV-20) at finite temperature, complementary to our recent study of the same system at T = 0 K [R. Binder and I. Burghardt, J. Chem. Phys. 152, 204120 (2020)]. Accurate quantum dynamical simulations are performed using the multi-layer multi-configuration time-dependent Hartree method as applied to a site-based Hamiltonian comprising 20 electronic states of Frenkel type and 460 vibrational modes, including site-local quinoid-distortion modes along with site-correlated bond-length alternation (BLA) modes, ring torsional modes, and an explicit harmonic-oscillator bath. A first-principles parameterized Frenkel-Holstein type Hamiltonian is employed, which accounts for correlations between the ring torsional modes and the anharmonically coupled BLA coordinates located at the same junction. Thermally induced fluctuations of the torsional modes are described by a stochastic mean-field approach, and their impact on the excitonic motion is characterized in terms of the exciton mean-squared displacement. A normal diffusion regime is observed under periodic boundary conditions, apart from transient localization features. Even though the polaronic exciton species are comparatively weakly bound, exciton diffusion is found to be a coherent-rather than hopping type-process, driven by the fluctuations of the soft torsional modes. Similar to the previous observations for oligothiophenes, the evolution for the most part exhibits a near-adiabatic dynamics of local exciton ground states (LEGSs) that adjust to the local conformational dynamics. However, a second mechanism, involving resonant transitions between neighboring LEGSs, gains importance at higher temperatures.

First-Principles Quantum and Quantum-Classical Simulations of Exciton Diffusion in Semiconducting Polymer Chains at Finite Temperature.

We report on first-principles quantum-dynamical and quantum-classical simulations of photoinduced exciton dynamics in oligothiophene chain segments, representative of intrachain exciton migration in the poly(3-hexylthiophene) (P3HT) polymer. Following up on our recent study (Binder R.; Burghardt, I. Faraday Discuss. 2020, 221, 406), multilayer multiconfiguration time-dependent Hartree calculations for a short oligothiophene segment comprising 20 monomer units (OT-20) are carried out to obtain full quantum-dynamical simulations at finite temperature. These are employed to benchmark mean-field Ehrenfest calculations, which are shown to give qualitatively correct results for the present system. Periodic boundary conditions turn out to significantly improve earlier estimates of diffusion coefficients. Using the Ehrenfest approach, a series of calculations are subsequently carried out for larger lattices (OT-40 to OT-80), leading to estimates for temperature-dependent mean-squared displacements, which are found to exhibit a near-linear dependence as a function of time. The resulting diffusion coefficient estimates are an increasing function of temperature, whose detailed functional form depends on the degree of static disorder. With a realistic static disorder parameter (σs ≃ 0.06 eV), the diffusion coefficients decrease from D ∼ 1 × 10-2 cm2 s-1 to D ∼ 1 × 10-3 cm2 s-1, in qualitative agreement with experimental data for P3HT. The dynamical scenario obtained from our simulations shows that exciton migration in P3HT-type chains is a largely adiabatic process throughout the temperature regime we investigated (i.e., T = 50-300 K). The resulting picture of exciton migration is a coherent, but not bandlike, motion of an exciton-polaron driven by fluctuations induced by low-frequency modes. This process acquires partial hopping character if static disorder becomes prominent and Anderson localization sets in.

First-principles description of intra-chain exciton migration in an oligo(para-phenylene vinylene) chain. II. ML-MCTDH simulations of exciton dynamics at a torsional defect.

The first-principles parameterized Frenkel-Holstein Hamiltonian developed in Paper I [R. Binder et al., J. Chem. Phys. 152, 204119 (2020)] is employed to carry out full quantum-dynamical simulations of an elementary exciton migration event in an oligo-(para-phenylene vinylene) chain with 20 repeat units (OPV-20). We consider a dynamic scenario where an initial torsional defect, creating a conjugation break, relaxes on a time scale of about 500 fs toward a planarized structure and triggers the spatial displacement of the photogenerated exciton. Accurate quantum dynamical simulations are performed using the multi-layer multi-configuration time-dependent Hartree method as applied to an OPV-20 system comprising 20 electronic states of Frenkel type and 60 vibrational modes. These include site-local quinoid-distortion modes, site-correlated bond-length alternation (BLA) modes, and an active ring torsional mode at the central junction. The simulations fully account for correlations between the ring torsional mode and the anharmonically coupled BLA coordinate located at the same junction. In accordance with our earlier studies of a related oligothiophene (OT) system [R. Binder, D. Lauvergnat, and I. Burghardt, Phys. Rev. Lett. 120, 227401 (2018)], these simulation results highlight that exciton migration is a coherent process driven by the fluctuations of "soft" modes, exemplified by the ring torsions. Conversely, these results also show that trapping due to high-frequency modes, leading to energetic stabilization of the exciton-polaron species, is weaker in OPV than in the OT system. This underscores not only the generic features of exciton dynamics in conjugated polymer systems, but also the role of molecular specificities.

First-principles description of intra-chain exciton migration in an oligo(para-phenylene vinylene) chain. I. Generalized Frenkel-Holstein Hamiltonian.

A generalized Frenkel-Holstein Hamiltonian is constructed to describe exciton migration in oligo(para-phenylene vinylene) chains, based on excited state electronic structure data for an oligomer comprising 20 monomer units (OPV-20). Time-dependent density functional theory calculations using the ωB97XD hybrid functional are employed in conjunction with a transition density analysis to study the low-lying singlet excitations and demonstrate that these can be characterized to a good approximation as a Frenkel exciton manifold. Based on these findings, we employ the analytic mapping procedure of Binder et al. [J. Chem. Phys. 141, 014101 (2014)] to translate one-dimensional (1D) and two-dimensional (2D) potential energy surface (PES) scans to a fully anharmonic, generalized Frenkel-Holstein (FH) Hamiltonian. A 1D PES scan is carried out for intra-ring quinoid distortion modes, while 2D PES scans are performed for the anharmonically coupled inter-monomer torsional and vinylene bridge bond length alternation modes. The kinetic energy is constructed in curvilinear coordinates by an exact numerical procedure, using the TNUM Fortran code. As a result, a fully molecular-based, generalized FH Hamiltonian is obtained, which is subsequently employed for quantum exciton dynamics simulations, as shown in Paper II [R. Binder and I. Burghardt, J. Chem. Phys. 152, 204120 (2020)].

Histological and Gene Expression Analysis of the Effects of Menopause Status and Hormone Therapy on the Vaginal Introitus and Labia Majora.

BACKGROUND: The study aimed to determine the effect of menopausal status and hormone therapy on the introitus and labia majora at the levels of histology and gene expression. METHODS: Three cohorts of 10 women each (pre-menopause, post-menopause and post-menopause + hormone therapy) were selected based on the presentation of clinical atrophy and vaginal pH. Biopsies were obtained from the introitus (fourchette) and labia majora and processed for histology and gene expression analyses with microarrays. Other data collected included self-assessed symptoms, serum estradiol, testosterone, serum hormone binding globulin and the pH of the vagina and labia majora. RESULTS: The introitus appears exquisitely sensitive to hormone status. Dramatic changes were observed in histology including a thinning of the epithelium in post-menopausal subjects with vaginal atrophy. Furthermore, there was differential expression of many genes that may contribute to tissue remodeling in the atrophic introitus. Levels of expression of genes associated with wound healing, angiogenesis, cell migration/locomotion, dermal structure, apoptosis, inflammation, epithelial cell differentiation, fatty acid, carbohydrate and steroid metabolism were significantly different in the cohort exhibiting atrophy of the introitus. While changes were also observed at the labia, that site was considerably less sensitive to hormone status. The gene expression changes observed at the introitus in this study were very similar to those reported previously in the atrophic vagina providing further evidence that these changes are associated with atrophy. CONCLUSIONS: The histological and gene expression changes occurring within the introitus after menopause may contribute to the constellation of symptoms that constitute the genitourinary syndrome of menopause.

First-principles quantum simulations of exciton diffusion on a minimal oligothiophene chain at finite temperature.

High-dimensional multiconfigurational quantum dynamics simulations are carried out at finite temperature to simulate exciton diffusion on an oligothiophene chain, representative of a segment of the poly(3-hexylthiophene) (P3HT) polymer. The ab initio parametrized site-based Hamiltonian of Binder et al. [Phys. Rev. Lett., 2018, 120, 227401] is employed to model a 20-site system, including intra-ring and inter-ring high-frequency modes as well as torsional modes which undergo thermal fluctuations induced by an explicit harmonic oscillator bath. The system-bath dynamics is treated within the setting of a stochastic mean-field Schrödinger equation. For the 20-site excitonic system, a total of 20 Frenkel states and 248 modes are propagated using the multi-layer multi-configuration time-dependent Hartree (ML-MCTDH) method. The resulting dynamics can be interpreted in terms of the coherent motion of an exciton-polaron quasi-particle stochastically driven by torsional fluctuations. This dynamics yields a near-linear mean squared displacement (MSD) as a function of time, from which a diffusion coefficient can be deduced which increases with temperature, up to 5.7 × 10-3 cm2 s-1 at T = 300 K.

Coherent Charge Transfer Exciton Formation in Regioregular P3HT: A Quantum Dynamical Study.

The ultrafast formation of charge transfer excitons (CTXs) in regioregular poly(3-hexyl thiophene) (rrP3HT) domains is elucidated by electronic structure and quantum dynamical studies of an aggregate model system comprising five stacked quaterthiophene units. Using a multistate vibronic coupling Hamiltonian parametrized by TDDFT calculations for 13 electronic states of Frenkel and CTX type, along with 78 vibrational modes, quantum dynamical simulations are carried out using the Multi-Layer Multi-Configuration Time-Dependent Hartree (ML-MCTDH) method. In line with time-resolved spectroscopic results [ De Sio , A. ; et al. Nat. Commun. 2016 , 7 , 13742 ], it is found that CTX formation occurs immediately upon photoexcitation, accompanied by sustained regular oscillations with a ∼22 fs periodicity. These coherent features, whose presence may seem surprising in a high-dimensional aggregate or thin film material, can be traced back to a dominant vibronic signature of CC stretch-type high-frequency modes. These vibrational signatures are found to be enhanced due to a collective vibronic response that is prompted by the initial generation of a delocalized bright exciton and its subsequent relaxation, by internal conversion, to a polaronic local exciton ground state.

CD91 on dendritic cells governs immunosurveillance of nascent, emerging tumors.

The immune system detects aberrant, premalignant cells and eliminates them before the development of cancer. Immune cells, including T cells, have been shown to be critical components in eradicating these aberrant cells, and when absent in the host, incidence of cancer increases. Here, we show that CD91, a receptor expressed on antigen-presenting cells, is required for priming immune responses to nascent, emerging tumors. In the absence of CD91, effector immune responses are subdued, and tumor incidence and progression are amplified. We also show that, consequently, tumors that arise in the absence of CD91 express neo-epitopes with indices that are indicative of greater immunogenicity. Polymorphisms in human CD91 that are expected to affect ligand binding are shown to influence antitumor immune responses in cancer patients. This study presents a molecular mechanism for priming immune responses to nascent, emerging tumors that becomes a predictor of cancer susceptibility and progression.

Complex Formation of the Tetracycline-Binding Aptamer Investigated by Specific Cross-Relaxation under DNP.

While dynamic nuclear polarization (DNP) under magic-angle spinning (MAS) is generally a powerful method capable of greatly enhancing the sensitivity of solid-state NMR spectroscopy, hyperpolarization also gives rise to peculiar spin dynamics. Here, we elucidate how specific cross-relaxation enhancement by active motions under DNP (SCREAM-DNP) can be utilized to selectively obtain MAS-NMR spectra of an RNA aptamer in a tightly bound complex with a methyl-bearing ligand (tetracycline) due to the effective CH3 -reorientation at an optimized sample temperature of approximately 160 K. SCREAM-DNP can spectrally isolate the complex from non-bound species in an RNA mixture. This selectivity allows for a competition assay between the aptamer and a mutant with compromised binding affinity. Variations in molecular structure and methyl dynamics, as observed by SCREAM-DNP, between free tetracycline and RNA-bound tetracycline are discussed.

Immunosurveillance of cancer and the heat shock protein-CD91 pathway.

The intracellular functions of heat shock proteins (HSPs) as chaperones of macromolecules are well known. Current observations point to a role of these chaperones in initiating and modulating immune responses to tumors via receptor(s) on dendritic cells. In this article we provide an insight into, and a basis for, the importance of these HSP-mediated immune responses in rejecting nascent and emerging tumors.

Cutting Edge: The Heat Shock Protein gp96 Activates Inflammasome-Signaling Platforms in APCs.

Several heat shock proteins (HSPs) prime immune responses, which are, in part, a result of activation of APCs. APCs respond to these immunogenic HSPs by upregulating costimulatory molecules and secreting cytokines, including IL-1ß. These HSP-mediated responses are central mediators in pathological conditions ranging from cancer, sterile inflammation associated with trauma, and rheumatoid arthritis. We tested in this study the requirement of inflammasomes in the release of IL-1ß by one immunogenic HSP, gp96. Our results show that murine APCs activate NLRP3 inflammasomes in response to gp96 by K+ efflux. This is shown to initiate inflammatory conditions in vivo in the absence of additional known inflammasome activators or infection. These results document a novel mechanism by which proteins of endogenous origin, the HSPs, can modulate an inflammatory response following their release from aberrant cells.

The symmetrical quasi-classical approach to electronically nonadiabatic dynamics applied to ultrafast exciton migration processes in semiconducting polymers.

In the last several years, a symmetrical quasi-classical (SQC) windowing model applied to the classical Meyer-Miller (MM) vibronic Hamiltonian has been shown to be a simple, efficient, general, and quite-accurate method for treating electronically nonadiabatic processes at the totally classical level. Here, the SQC/MM methodology is applied to ultrafast exciton dynamics in a Frenkel/site-exciton model of oligothiophene (OT) as a model of organic semiconductor polymers. In order to keep the electronic representation as compact and efficient as possible, the adiabatic version of the MM Hamiltonian was employed, with dynamical calculations carried out in the recently developed "kinematic momentum" representation, from which site/monomer-specific (diabatic) excitation probabilities were extracted using a new procedure developed in this work. The SQC/MM simulation results are seen to describe coherent exciton transport driven by planarization of a central torsion defect in the OT oligomer as well as to capture exciton self-trapping effects in good agreement with benchmark quantum calculations using the multi-layer multiconfiguration time-dependent Hartree approach. The SQC/MM calculations are also seen to significantly outperform the standard Ehrenfest approach, which shows serious discrepancies. These results are encouraging, not only because they illustrate a significant further application of the SQC/MM approach and its utility, but because they strongly suggest that classical mechanical simulations (with the potential for linear scaling efficiency) can be used to capture, quantitatively, important dynamical features of electronic excitation energy transfer in semiconducting polymers.