The effects of glycemic index on prostate cancer progression in a xenograft mouse model.

BACKGROUND: Previously, we found low-carbohydrate diets slowed prostate cancer (PC) growth and increased survival vs. a Western diet in mice, by inhibiting the insulin/IGF-1 axis. Thus, we tested whether modifying carbohydrate quality to lower glycemic index (GI) without changing quantity results in similar benefits as with reduced quantity. METHODS: Male SCID mice injected with LAPC-4 cells were single-housed and randomized when their tumors reached 200 mm3 on average to a LoGI (48% carbohydrate kcal, from Hylon-VII) or HiGI Western diet (48% carbohydrate kcal, from sucrose). Body weight and tumor volume were measured weekly. Body composition was assessed 35 days after randomization. Blood glucose and serum insulin, IGF-1 and IGFBP3 were measured at study end when tumor volumes reached 800 mm3. We analyzed gene expression of mice tumors by RNA-sequencing and human tumors using the Prostate Cancer Transcriptome Atlas. RESULTS: There were no significant differences in tumor volume (P > 0.05), tumor proliferation (P = 0.29), and overall survival (P = 0.15) between groups. At 35 days after randomization, the LoGI group had 30% lower body fat (P = 0.007) despite similar body weight (P = 0.58). At sacrifice, LoGI mice had smaller livers (P < 0.001) and lower glucose (P = 0.15), insulin (P = 0.11), IGF-1 (P = 0.07) and IGF-1:IGFBP3 ratio (P = 0.05), and higher IGFBP3 (P = 0.09) vs. HiGI, although none of these metabolic differences reached statistical significance. We observed differential gene expression and pathway enrichment in mice tumors by diet. The most upregulated and downregulated gene in the LoGI group showed expression patterns more closely resembling expression in human benign prostate tissue vs. PC. CONCLUSIONS: In this single mouse xenograft model, consuming a low GI diet did not delay PC growth or survival vs. a high GI diet despite suggestions of decreased activation of the insulin/IGF-1 pathway. These data suggest that improving carbohydrate quality alone while consuming a high carbohydrate diet may not effectively slow PC growth.

Stimulation of antitumor immunity by FoxP3-targeting PROTAC.

CD4 + regulatory T cells (Tregs) play a central role in regulating and suppressing anti-tumor immune responses. FoxP3 is a transcription factor and master regulator of the Treg lineage. We developed and characterized a proteolysis targeting chimeric (PROTAC) drug that targets FoxP3 (PF). PF was created by linking the FoxP3 binding peptide P60 to pomalidomide, a ligand for E3 ligase. Ternary complex formation between PF, FoxP3, and cereblon (component of an E3 ligase) was confirmed using surface plasmon resonance assay (cooperativity factor of 2.27). PF decreased mouse and human FoxP3 expression in vitro in a proteasome-dependent manner. In mice, PF decreased FoxP3 in both the spleen and peripheral lymphocytes. PF-treated lymphocytes (human or mice) were better at stimulating CD8 + lymphocyte proliferation and activation. PF treatment decreased RENCA tumor growth in mice. PF enhanced antitumor immunity associated with αPD1 or mTOR inhibitor (mTORi). Lymphocytes from mice treated with PF and mTORi showed reduced metastatic tumor growth in untreated mice, providing further evidence for an adaptive immune response as the mechanism of action. We showed that PF binds FoxP3 and decreases FoxP3 expression in Tregs, reducing Treg function and generating antitumor immunity.

PAK4 inhibition improves PD1 blockade immunotherapy in prostate cancer by increasing immune infiltration.

Antitumor immunity requires lymphocytes to localize to the tumor. Prostate cancers (PCs) are immunologically cold and tend to lack T-cell infiltration. Most advanced PCs are insensitive to PD1 blockade therapies. Using syngeneic RM1 prostate tumors, p21-activated kinase-4 (PAK4) knockdown (KD) and pharmacological inhibition was assessed in C57BL/6J mice treated with PD1 antibodies (αPD1). RNASeq was used to characterize the immune response in the tumor. Immunohistochemistry, flow cytometry, and in vivo blocking studies confirmed the role of cell surface proteins in the generation of immune responses. In The Cancer Genome Atlas, PAK4 expression was inversely correlated with immune cell infiltration. PAK4 expression was controlled by the androgen receptor and its pioneering factor, FOXA1. PAK4 KD increased CD8+ T-cell infiltration and expression of IFNγ response genes. PAK4 KD also upregulated angiogenesis and endothelial cell adhesion molecules in the tumor microenvironment, contributing to CD8+ lymphocyte recruitment. Pharmacological inhibition of PAK4 made PC more responsive to immunotherapy with αPD1. A decrease in PAK4 activity increases immune activation and vascularity, which increases CD8+ lymphocyte infiltration into the tumor. Therefore, targeting PAK4 may improve the response of human PC to immunotherapy.

Hypoxia-inducible factor pathway genes predict survival in metastatic clear cell renal cell carcinoma.

PURPOSE: Hypoxia inducible factor (HIF) pathway alterations drive progression of clear cell renal cell carcinoma (ccRCC). We aim to evaluate genes within the canonical and non-canonical HIF pathways as predictors of survival in metastatic ccRCC. MATERIALS AND METHODS: Gene expression was determined from 324 archival pretreatment nephrectomy specimens from CALGB90206, a phase III trial of patients treated with interferon alpha (INF-α) vs. INF-α plus bevacizumab. TaqMan RT-qPCR was performed using RNA from tumors macrodissected based on review by genitourinary pathology. RESULTS: A total of 35 HIF-related genes were assessed by Cox regression analysis. After adjusting for sex and Memorial Sloan Kettering Cancer Center risk score (MSKCC-RS), 11 genes predicted OS: HIF2A (HR 1.059, P = 0.012), EGLN3 (HR 1.089, P = 0.012), VEGFC (HR 0.904, P = 0.039), VEGFD (HR 1.085, P = 0.016), FLT4 (HR 1.093, P = 0.038), CCND1 (HR 1.077, P = 0.026), TGFA (HR 1.127, P = 0.003), EGFR (HR 1.151, P = 0.028), VHL (HR 0.764, P = 0.002), HSP90AA1 (HR 0.845, P = 0.002), and PTEN (HR 1.163, P = 0.050); 7 genes predicted PFS: HIF2A (HR 1.060, P = 0.011), CCND1 (HR 1.082, P = 0.016), TGFA (HR 1.096, P = 0.026), EP300 (HR 1.171, P = 0.031), VHL (HR 0.775, P = 0.007), HSP90AA1 (HR 0.871, P = 0.015), and TP53 (HR 1.119, P = 0.050). Most of these genes validated as significant predictors of survival in the external, TCGA dataset. In multivariate analysis of all externally validated genes, VEGFC (HR 0.906, P = 0.043), TGFA (HR 1.122, P = 0.003), CITED2 (HR 1.113, P = 0.035) and EP300 (HR 1.136, P = 0.049) predicted OS; and HIF2A (HR 1.049, P = 0.036) and EP300 (HR 1.199, P = 0.010) predicted PFS. EGLN3 (HR 1.156, P = 0.045) and BNIP3 (HR 1.254, P = 0.049) significantly interacted with treatment status and predicted PFS in patients treated with IFN-α and IFN-α+bevacizumab, respectively. CONCLUSIONS: We identified specific gene isoforms in both the canonical and non-canonical HIF pathways associated with metastatic RCC survival. EGLN3 and BNIP3 showed significant interaction with treatment arm and may be predictive of treatment response. We have identified genes for future prospective investigation as predictive biomarkers and novel drug targets.

Low-Lying Electronic States of the Nickel Dimer.

The generalized Van Vleck second order multireference perturbation theory (GVVPT2) method was used to investigate the low-lying electronic states of Ni2. Because the nickel atom has an excitation energy of only 0.025 eV to its first excited state (the least in the first row of transition elements), Ni2 has a particularly large number of low-lying states. Full potential energy curves (PECs) of more than a dozen low-lying electronic states of Ni2, resulting from the atomic combinations 3F4 + 3F4 and 3D3 + 3D3, were computed. In agreement with previous theoretical studies, we found the lowest lying states of Ni2 to correlate with the 3D3 + 3D3 dissociation limit, and the holes in the d-subshells were in the subspace of delta orbitals (i.e., the so-dubbed δδ-states). In particular, the ground state was determined as X 1Γg and had spectroscopic constants: bond length (R e) = 2.26 Å, harmonic frequency (ωe) = 276.0 cm-1, and binding energy (D e) = 1.75 eV; whereas the 1 1Σg + excited state (with spectroscopic constants: R e = 2.26 Å, ωe = 276.8 cm-1, and D e = 1.75) of the 3D3 + 3D3 dissociation channel lay at only 16.4 cm-1 (0.002 eV) above the ground state at the equilibrium geometry. Inclusion of scalar relativistic effects through the spin-free exact two component (sf-X2C) method reduced the bond lengths of both of these two states to 2.20 Å, and increased their binding energies to 1.95 eV and harmonic frequencies to 296.0 cm-1 for X 1Γg and 297.0 cm-1 for 1 1Σg +. These values are in good agreement with experimental values of R e = 2.1545 ± 0.0004 Å, ωe = 280 ± 20 cm-1, and D 0 = 2.042 ± 0.002 eV for the ground state. All states considered within the 3F4 + 3F4 dissociation channel proved to be energetically high-lying and van der Waals-like in nature. In contrast to most previous theoretical studies of Ni2, full PECs of all considered electronic states of the molecule were produced.

Phonon-Driven Energy Relaxation in PbS/CdS and PbSe/CdSe Core/Shell Quantum Dots.

We study the impact of the chemical composition on phonon-mediated exciton relaxation in the core/shell quantum dots (QDs), with 1 nm core made of PbX and the monolayer shell made of CdX, where X = S and Se. For this, time-domain nonadiabatic molecular dynamics (NAMD) based on density functional theory (DFT) and surface hopping techniques are applied. Simulations reveal twice faster energy relaxation in PbS/CdS than PbSe/CdSe because of dominant couplings to higher-energy optical phonons in structures with sulfur anions. For both QDs, the long-living intermediate states associated with the core-shell interface govern the dynamics. Therefore, a simple exponential model is not appropriate, and the four-state irreversible kinetic model is suggested instead, predicting 0.9 and 0.5 ps relaxation rates in PbSe/CdSe and PbS/CdS QDs, respectively. Thus, 2 nm PdSe/CdSe QDs with a single monolayer shell exhibit the phonon-mediated relaxation time sufficient for carrier multiplications to outpace energy dissipation and benefit the solar conversion efficiency.

Accurate Dissociation of Chemical Bonds Using DFT-in-DFT Embedding Theory with External Orbital Orthogonality.

Our recent density functional theory (DFT)-in-DFT embedding protocol, which enforces intersubsystem (or external orbital) orthogonality, is used for the first time to investigate covalent bond dissociation and is shown to do so accurately. Full potential energy curves for the dissociation of a H-O bond in H2O and the C-C bond in H3C-CH3 have been constructed using the new embedding method, as have the challenging ionic bonds in LiH and LiF, and were found to match the reference Kohn-Sham (KS)-DFT curves to at least one part in 106. The added constraint of external orbital orthogonality allows for the formulation of an embedding protocol that does not rely on approximate kinetic energy functionals for the evaluation of the so-called nonadditive kinetic potential, does not introduce compensatory potentials, and does not require a total system calculation at any stage. The present work extends the demonstrated applicability of the external orthogonality variant of embedding theory by more than a factor of 2 to the interaction strength range of strong single bonds. In particular, it is demonstrated that homolytic cleavage of both covalent and ionic bonds into radicals can be accomplished.

Surface Chemistry of Semiconducting Quantum Dots: Theoretical Perspectives.

Colloidal quantum dots (QDs) are near-ideal nanomaterials for energy conversion and lighting technologies. However, their photophysics exhibits supreme sensitivity to surface passivation and defects, of which control is problematic. The role of passivating ligands in photodynamics remains questionable and is a focus of ongoing research. The optically forbidden nature of surface-associated states makes direct measurements on them challenging. Therefore, computational modeling is imperative for insights into surface passivation and its impact on light-driven processes in QDs. This Account discusses challenges and recent progress in understanding surface effects on the photophysics of QDs addressed via quantum-chemical calculations. We overview different methods, including the effective mass approximation (EMA), time-dependent density functional theory (TDDFT), and multiconfiguration approaches, considering their strengths and weaknesses relevant to modeling of QDs with a complicated surface. We focus on CdSe, PbSe, and Si QDs, where calculations successfully explain experimental trends sensitive to surface defects, doping, and ligands. We show that the EMA accurately describes both linear and nonlinear optical properties of large-sized CdSe QDs (>2.5 nm), while TDDFT is required for smaller QDs where surface effects dominate. Both approaches confirm efficient two-photon absorption enabling applications of QDs as nonlinear optical materials. TDDFT also describes the effects of morphology on the optical response of QDs: the photophysics of stoichiometric, magic-sized XnYn (X = Cd, Pb; Y = S, Se) QDs is less sensitive to their passivation compared with nonstoichiometric Xn≠mYm QDs. In the latter, surface-driven optically inactive midgap states can be eliminated by anionic ligands, explaining the better emission of metal-enriched QDs compared with nonmetal-enriched QDs. Ideal passivation of magic-sized QDs by amines and phosphine oxides leaves lower-energy transitions intact, while thiol derivatives add ligand-localized trap states to the band gap. Depending on its position, any loss of ligand from the QD's surface also introduces electron or hole traps, decreasing the QD's luminescence. TDDFT investigations of QD-ligand and QD-QD interactions provide an explanation of experimentally detected enhancement of blinking on-times in closely packed Si QDs and establish favorable conditions for hole transfer from the photoexcited CdSe QD to metal-organic dyes. While TDDFT well describes qualitative trends in optical response to stoichiometry and ligand modifications of QDs, it is unable to calculate highly correlated electronic states like biexcitons and magnetic-dopant-derived states. In these cases, multiconfiguration methods are applied to small nanoclusters and the results are extrapolated to larger-sized QDs, providing reasonable explanations of experimental observables. For light-driven dynamics, the electron-phonon couplings are important, and nonadiabatic dynamics (NAD) is applied. NAD based on first-principles calculations is a current grand challenge for the theory. However, it can be accomplished through sets of semiclassical approximations such as surface hopping (SH). We discuss validations of approximations used in photodynamics of ligated and doped QDs. Time-domain DFT-based SH-NAD reveals the ligand's role in ultrafast energy relaxation and the connection between the phonon bottleneck and the Zeno effect in CdSe QDs. The calculated results are helpful in controlling both dissipation and radiative processes in QDs via surface engineering and in explanations of experimental data.

Computational insights into CdSe quantum dots' interactions with acetate ligands.

Using density functional theory (DFT) and time-dependent DFT (TDDFT), we investigate the effects of carboxylate groups on the electronic and optical properties of CdSe quantum dots (QDs). We specifically focus on the mechanisms of the binding of the acetate anion to the QD surface with and without excess of Cd(2+) cations. Our calculations show that the most stable ligated conformations are those where an acetate is attached to extra Cd(2+) ion forming a [Cd(2+)(CH3COO(-))] at the QD's surface, while also accompanied by an acetate attached nearby at the surface balancing the overall neutral charge of the system. In contrast, formation of a neutral metal-acetate complex [Cd(2+)(CH3COO(-))2] at the QD surface is found to be the least energetically preferable. A strength of the QD-ligand interaction depends on the solvent, the facet of the QD to which the ligands are attached, and the binding mode - with the bridging mode found to be the most stable conformation for both acetate and cadmium acetate ligands. The cadmium acetate ligands introduce electron trap states at the edge of the conduction band - unoccupied orbitals predominately localized on Cd(2+) ion - that are extremely sensitive to the ligand position and the solvent polarity. Polar solvents like acetonitrile delocalize the electronic density over the entire system and, thus, eliminate trap states. As a result, mixed passivation of the CdSe QDs by pairs of cadmium acetate and acetate ligands provides optimal optical properties with minimal contributions of the ligand-related trap states and optically bright lowest energy transitions.

Density differences in embedding theory with external orbital orthogonality.

First results on electron densities and energies for a number of molecular complexes with different interaction strengths (ranging from ca. 0.3 to 40 kcal/mol), obtained using our recently introduced DFT-in-DFT embedding equations (i.e., Kohn-Sham equations with constrained electron density (KSCED) and external orbital orthogonality (ext orth), KSCED(x, ext orth), where x denotes the single particle support: monomer (m); supermolecular (s); or extended monomer (e)) are compared with densities from supermolecular Kohn-Sham (KS)-DFT calculations and traditional DFT-in-DFT results. Because our methodology does not rely on error-prone potentials that are not present in supermolecular KS-DFT calculations, it allows DFT-in-DFT calculations to achieve much higher accuracy than previous protocols of DFT-in-DFT that employed such potentials. It is shown that whereas conventional DFT-in-DFT embedding theory leads to errors in the electron density at the boundary between subsystems, the situation is remedied when orbital orthogonality between subsystems (i.e., external orthogonality) is enforced. Our approach reproduces KS-DFT total energies at least to the seventh decimal place (and exactly at most geometries) for the tested systems. Potential energy curves (PECs) of the separation of some of the tested systems into fragments are calculated. PECs, obtained with the new equations, using the usual Kohn-Sham equations with constrained electron density and supermolecular basis expansion [KSCED(s, ext orth, v(T) = 0), where v(T) is the nonadditive kinetic potential] were found to be virtually identical to those from conventional KS-DFT; equilibrium distances and interaction energies were reproduced to all reported digits for both local density approximation (LDA) and generalized gradient approximation (GGA) functionals. As an additional approximation, an alternative one-particle space (to the common monomer or supermolecular spaces) in which KS orbitals of a subsystem are expanded is introduced. This expansion, which we refer to as the extended monomer expansion [e.g., KSCED(e)], includes basis functions centered on atom(s) of the complementary subsystem in the interfacial region. Density differences and PECs obtained with the new equations and new one-particle space [i.e., KSCED(e, ext orth, v(T) = 0)] were closely related to those obtained from KSCED(s, ext orth, v(T) = 0). The new approach does not require any supermolecular calculations.

Relativistic GVVPT2 multireference perturbation theory description of the electronic states of Y2 and Tc2.

The multireference generalized Van Vleck second-order perturbation theory (GVVPT2) method is used to describe full potential energy curves (PECs) of low-lying states of second-row transition metal dimers Y(2) and Tc(2), with scalar relativity included via the spin-free exact two-component (sf-X2C) Hamiltonian. Chemically motivated incomplete model spaces, of the style previously shown to describe complicated first-row transition metal diatoms well, were used and again shown to be effective. The studied states include the previously uncharacterized 2(1)Σ(g)(+) and 3(1)Σ(g)(+) PECs of Y(2). These states, together with 1(1)Σ(g)(+), are relevant to discussion of controversial results in the literature that suggest dissociation asymptotes that violate the noncrossing rule. The ground state of Y(2) was found to be X(5)Σ(u)(­) (similar to Sc(2)) with bond length R(e) = 2.80 Å, binding energy D(e) = 3.12 eV, and harmonic frequency ω(e) = 287.2 cm(­1), whereas the lowest 1(1)(g)(+) state of Y(2) was found to lie 0.67 eV above the quintet ground state and had spectroscopic constants R(e) = 3.21 Å, D(e) = 0.91 eV, and ω(e) = 140.0 cm(­1). Calculations performed on Tc(2) include study of the previously uncharacterized relatively low-lying 1(5)Σ(g)(+) and 1(9)Σ(g)(+) states (i.e., 0.70 and 1.84 eV above 1(1)Σ(g)(+), respectively). The ground state of Tc(2) was found to be X(3)Σ(g)(­) with R(e) = 2.13 Å, D(e) = 3.50 eV, and ω(e) = 336.6 cm(­1) (for the most stable isotope, Tc-98) whereas the lowest (1)Σ(g)(+) state, generally accepted to be the ground state symmetry for isovalent Mn(2) and Re(2), was found to lie 0.47 eV above the X(3)Σ(g)(­) state of Tc(2). The results broaden the range of demonstrated applicability of the GVVPT2 method.

GVVPT2 multireference perturbation theory description of diatomic scandium, chromium, and manganese.

With relatively simple model spaces derived from valence bond models, a straightforward zero-order Hamiltonian, and the use of moderate-sized Dunning-type correlation consistent basis sets (cc-pVTZ, aug-cc-pVTZ, and cc-pVQZ), the second order generalized Van Vleck perturbation theory (GVVPT2) method is shown to produce potential energy curves (PECs) and spectroscopic constants close to experimental results for both ground and low-lying excited electronic states of Sc(2), Cr(2) and Mn(2). In spite of multiple quasidegeneracies (particularly for the cases of Sc(2) and Mn(2)), the GVVPT2 PECs are smooth with no discontinuities. Since these molecules have been identified as ones that widely used perturbative methods are inadequate for describing well, due to intruder state problems, unless shift parameters are introduced that can obfuscate the physics, this study suggests that the conclusion about the inadequacy of multireference perturbation theory be re-evaluated. The ground state of Sc(2) is predicted to be X(5)∑(u)(-), and its spectroscopic constants are close to the ones at the MRCISD level. Near equilibrium geometries, the 1(3)∑(u)(-) electronic state of Sc(2) is found to be less stable than the quintet ground state by 0.23 eV. The Cr(2) PEC has several features of the Rydberg-Klein-Rees (RKR) experimental curve (e.g., the pronounced shelf at elongated bond lengths), although the predicted bond length is slightly long (R(e) = 1.80 Å with cc-pVQZ compared to the experimental value of 1.68 Å). The X(1)∑(g)(+) ground state of Mn(2) is predicted to be a van der Waals molecule with a long bond length, R(e), of 3.83 Å using a cc-pVQZ basis set (experimental value = 3.40 Å) and a binding energy, D(e), of only 0.05 eV (experimental value = 0.1 eV). We obtained R(e) = 3.40 Å and D(e) = 0.09 eV at the complete basis set (CBS) limit for ground state Mn(2). Low lying excited state curves have also been characterized for all three cases (Cr(2), Mn(2), and Sc(2)) and show similar mathematical robustness as the ground states. These results suggest that the GVVPT2 multireference perturbation theory method is more broadly applicable than previously documented.