FoxA1/2-dependent epigenomic reprogramming drives lineage switching in lung adenocarcinoma.

The ability of cancer cells to alter their identity is essential for tumor survival and progression. Loss of the pulmonary lineage specifier NKX2-1 within KRAS-driven lung adenocarcinoma (LUAD) enhances tumor progression and results in a pulmonary-to-gastric lineage switch that is dependent upon the activity of pioneer factors FoxA1 and FoxA2; however, the underlying mechanism remains largely unknown. Here, we show that FoxA1/2 reprogram the epigenetic landscape of NKX2-1-negative LUAD to facilitate a gastric identity. After Nkx2-1 deletion, FoxA1/2 mediate demethylation of gastric-defining genes through recruitment of TET3, an enzyme that induces DNA demethylation. H3K27ac ChIP-seq and HiChIP show that FoxA1/2 also control the activity of regulatory elements and their 3D interactions at gastric loci. Furthermore, oncogenic KRAS is required for the FoxA1/2-dependent epigenetic reprogramming. This work demonstrates the role of FoxA1/2 in rewiring the methylation and histone landscape and cis-regulatory dynamics of NKX2-1-negative LUAD to drive cancer cell lineage switching.

Bowl-shaped Cluster CuB12 - : A Viable Global Minimum with Twofold Aromaticity.

A low-lying structure is revealed for the CuB12 - cluster, which is bowl-shaped. It consists of a triangular CuB2 base and a B10 rim. Molecular dynamics simulations indicates its structural robustness; at an elevated temperature (600 K), the base rotates reversibly within the B10 perimeter. Chemical bonding analysis detects 2σ- and 3π-delocalized bonds, suggesting double aromaticity. This is also confirmed by two diatropic and concentric ring currents under an external magnetic field.

FoxA1 and FoxA2 control growth and cellular identity in NKX2-1-positive lung adenocarcinoma.

Changes in cellular identity (also known as histologic transformation or lineage plasticity) can drive malignant progression and resistance to therapy in many cancers, including lung adenocarcinoma (LUAD). The lineage-specifying transcription factors FoxA1 and FoxA2 (FoxA1/2) control identity in NKX2-1/TTF1-negative LUAD. However, their role in NKX2-1-positive LUAD has not been systematically investigated. We find that Foxa1/2 knockout severely impairs tumorigenesis in KRAS-driven genetically engineered mouse models and human cell lines. Loss of FoxA1/2 leads to the collapse of a dual-identity state, marked by co-expression of pulmonary and gastrointestinal transcriptional programs, which has been implicated in LUAD progression. Mechanistically, FoxA1/2 loss leads to aberrant NKX2-1 activity and genomic localization, which in turn actively inhibits tumorigenesis and drives alternative cellular identity programs that are associated with non-proliferative states. This work demonstrates that FoxA1/2 expression is a lineage-specific vulnerability in NKX2-1-positive LUAD and identifies mechanisms of response and resistance to targeting FoxA1/2 in this disease.

Evidence of carbon-supported porphyrins pyrolyzed for the oxygen reduction reaction keeping integrity.

Fe(III) 5,10,15,20-(tetraphenyl)porphyrin chloride (FeTPP) and Co(III) 5,10,15,20-(tetraphenyl)porphyrin chloride (CoTPP) were adsorbed on carbon Vulcan and studied as electrocatalysts for the oxygen reduction reaction (ORR) before and after pyrolysis. The pyrolysis process was also simulated through ab initio molecular dynamic simulations and the minimum energy path for the O2 dissociation after the interaction with the metal center of the FeTPP and CoTPP were calculated. After the pyrolysis the FeTPP showed the best performances reducing O2 completely to H2O with increased limiting current and lower overpotential. Tafel slops for the various catalysts did not change after the pyrolytic process suggesting that the mechanism for the ORR is not affected by the heat treatment. TEM images, X-ray diffraction, XPS spectroscopy, 57Fe Mössbauer, and DFT simulations, suggest that there is no breakdown of the macrocyclic complex at elevated temperatures, and that the macro cyclic geometry is preserved. Small variations in the Metal-O2 (M-O2) binding energies and the M-N bond length were observed which is attributed to the dispersive interaction between the macrocycles and the irregular surface of the Vulcan substrate induced by the heat treatment and causing better interaction with the O2 molecule. The theoretical strategy herein applied well simulate and explain the nature of the M-N-C active sites and the performances towards the ORR.

Planar Elongated B12 Structure in M3B12 Clusters (M = Cu-Au).

Here, it is shown that the M3B12 (M = Cu-Au) clusters' global minima consist of an elongated planar B12 fragment connected by an in-plane linear M3 fragment. This result is striking since this B12 planar structure is not favored in the bare cluster, nor when one or two metals are added. The minimum energy structures were revealed by screening the potential energy surface using genetic algorithms and density functional theory calculations. Chemical bonding analysis shows that the strong electrostatic interactions with the metal compensate for the high energy spent in the M3 and B12 fragment distortion. Furthermore, metals participate in the delocalized π-bonds, which infers an aromatic character to these species.

Cluster Assembled Silicon-Lithium Nanostructures: A Nanowire Confined Inside a Carbon Nanotube.

We computationally explore an alternative to stabilize one-dimensional (1D) silicon-lithium nanowires (NWs). The Li12Si9 Zintl phase exhibits the NW [ Li 6 Si 5 ] ∞ 1 , combined with Y-shaped Si4 structures. Interestingly, this NW could be assembled from the stacking of the Li6Si5 aromatic cluster. The [ Li 6 Si 5 ] ∞ 1 @CNT nanocomposite has been investigated with density functional theory (DFT), including molecular dynamics simulations and electronic structure calculations. We found that van der Waals interaction between Li's and CNT's walls is relevant for stabilizing this hybrid nanocomposite. This work suggests that nanostructured confinement (within CNTs) may be an alternative to stabilize this free NW, cleaning its properties regarding Li12Si9 solid phase, i.e., metallic character, concerning the perturbation provided by their environment in the Li12Si7 compound.

Oxygen Reduction Reaction at Penta-Coordinated Co Phthalocyanines.

From the early 60s, Co complexes, especially Co phthalocyanines (CoPc) have been extensively studied as electrocatalysts for the oxygen reduction reaction (ORR). Generally, they promote the 2-electron reduction of O2 to give peroxide whereas the 4-electron reduction is preferred for fuel cell applications. Still, Co complexes are of interest because depending on the chemical environment of the Co metal centers either promote the 2-electron transfer process or the 4-electron transfer. In this study, we synthetized 3 different Co catalysts where Co is coordinated to 5 N atoms using CoN4 phthalocyanines with a pyridine axial linker anchored to carbon nanotubes. We tested complexes with electro-withdrawing or electro-donating residues on the N4 phthalocyanine ligand. The catalysts were characterized by EPR and XPS spectroscopy. Ab initio calculations, Koutecky-Levich extrapolation and Tafel plots confirm that the pyridine back ligand increases the Co-O2 binding energy, and therefore promotes the 4-electron reduction of O2. But the presence of electron withdrawing residues, in the plane of the tetra N atoms coordinating the Co, does not further increase the activity of the compounds because of pull-push electronic effects.

Self-compensation in chlorine-doped CdTe.

Defect energetics, charge transition levels, and electronic band structures of several Cl-related complexes in CdTe are studied using density-functional theory calculations. We investigate substitutional chlorine (ClTe and ClCd) and complexes formed by ClTe with the cadmium vacancy (ClTe-VCd and 2ClTe-VCd) and the TeCd antisite (ClTe-TeCd). Our calculations show that none of the complexes studied induce deep levels in the CdTe band gap. Moreover, we find that ClTe-VCd and ClTe are the most stable Cl-related centers in n-type and p-type CdTe, under Te-rich growth conditions, showing shallow donor and acceptor properties, respectively. This result suggests that the experimentally-observed Fermi level pinning near midgap would be originated in self-compensation. We also find that the formation of the ClTe-TeCd complex passivates the deep level associated to the Te antisite in neutral charge state.

(Li6 Si5 )2-5 : The Smallest Cluster-Assembled Materials Based on Aromatic Si5 6- Rings.

Extensive explorations of their potential energy surfaces, combined with high-level quantum chemical computations, strikingly show that the lowest energy structures of the (Li6 Si5 )2-5 systems consist of 2-5 Si5 6- aromatic units, surrounded by Li+ counterions, respectively. These viable gas-phase compounds are the pioneering reported cases of oligomers made by planar aromatic silicon rings. Based on the key evidence that these oligomers are energetically favored, and that their silicon rings aromaticity is thoroughly preserved, the Li6 Si5 cluster is proposed as a potential assembly unit to build silicon-lithium nanostructures, thus opening new paths to design Zintl compounds at the nanoscale level.

Transient external force induces phenotypic reversion of malignant epithelial structures via nitric oxide signaling.

Non-malignant breast epithelial cells cultured in three-dimensional laminin-rich extracellular matrix (lrECM) form well organized, growth-arrested acini, whereas malignant cells form continuously growing disorganized structures. While the mechanical properties of the microenvironment have been shown to contribute to formation of tissue-specific architecture, how transient external force influences this behavior remains largely unexplored. Here, we show that brief transient compression applied to single malignant breast cells in lrECM stimulated them to form acinar-like structures, a phenomenon we term 'mechanical reversion.' This is analogous to previously described phenotypic 'reversion' using biochemical inhibitors of oncogenic pathways. Compression stimulated nitric oxide production by malignant cells. Inhibition of nitric oxide production blocked mechanical reversion. Compression also restored coherent rotation in malignant cells, a behavior that is essential for acinus formation. We propose that external forces applied to single malignant cells restore cell-lrECM engagement and signaling lost in malignancy, allowing them to reestablish normal-like tissue architecture.

Energetics and diffusion of liquid water and hydrated ions through nanopores in graphene: ab initio molecular dynamics simulation.

The energetics and diffusion of water molecules and hydrated ions (Na+, Cl-) passing through nanopores in graphene are addressed by dispersion-corrected density functional theory calculations and ab initio molecular dynamics (MD) simulations. Pores of about 0.8 nm in diameter with different pore-edge passivations, with (H) and (O, H) atoms, were considered. Our MD simulations show a water flux through the hydroxylated pores of about one H2O molecule every three picoseconds, in close agreement with recent experiments that estimated a water flux of three molecules per picosecond through pores of ∼1 nm. We also find that both pores are effective in blocking hydrated Na+ and Cl- ions with large energy barriers, ranging from 12 to 15 eV. In addition, pore passivation with O atoms would increase the water transport through hydroxylated pores, due to the formation of hydrogen bonds with nearby water molecules, which is not observed in the hydrogenated pores.